https://gatk.broadinstitute.org/hc/en-us 2026-04-03T06:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360035530752-What-types-of-variants-can-GATK-tools-detect-or-handle 2024-06-25T07:15:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035530772-Can-I-use-different-versions-of-the-GATK-at-different-steps-of-my-analysis 2024-06-25T07:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360035530792-How-should-I-prepare-for-a-GATK-workshop 2024-06-25T07:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360035530852-How-should-I-cite-GATK-in-my-own-publications 2024-07-08T19:44:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035530892-GATK-on-Google-Cloud 2024-06-25T07:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360035530932-GATK-on-Alibaba-Cloud 2024-06-25T07:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035530952--How-to-Execute-Workflows-from-the-gatk-workflows-Git-Organization 2025-07-15T14:32:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531012--How-to-Filter-on-genotype-using-VariantFiltration 2024-06-25T07:15:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531092--How-to-part-I-Sensitively-detect-copy-ratio-alterations-and-allelic-segments 2025-06-02T16:43:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering 2025-01-22T14:29:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2 2024-06-25T07:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-rare-germline-copy-number-variants 2025-10-23T14:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531392-Difference-between-QUAL-and-GQ-annotations-in-germline-variant-calling 2024-06-25T07:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell 2024-06-25T07:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531432-Genotype-Refinement-workflow-for-germline-short-variants 2024-06-25T07:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531452-After-gCNV-calling-considerations 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531532-HaplotypeCaller-Reference-Confidence-Model-GVCF-mode 2024-06-25T07:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531572-Evaluating-the-quality-of-a-germline-short-variant-callset 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR 2024-06-25T07:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531632-Hardware-optimizations-SSD-CPU-GPU-FPGA-TPU 2024-06-25T07:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Reference-genome-format 2024-06-25T07:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format 2024-06-25T07:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format 2024-06-25T07:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531712-HDF5-format 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531732-Funcotator-Annotation-Specifications 2025-09-08T16:47:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531752-Google-Dataproc-Spark-cluster-service 2024-06-25T07:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531772-Docker-container-image-registry 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531792-Paired-end-or-mate-pair 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format 2024-06-25T07:17:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531832-Bisulfite-sequencing-Cytosine-methylation 2024-06-25T07:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists 2024-12-04T13:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531872-Phred-scaled-quality-scores 2026-03-30T12:25:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531892-GATK4-command-line-syntax 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531932-Pre-adapter-artifacts-in-hybrid-selection-Bait-bias 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531952-Rank-Sum-Test 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format 2024-06-25T07:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360035531992-Inbreeding-Coefficient 2024-06-25T07:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532012-Parallelism-Multithreading-Scatter-Gather 2024-06-25T07:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532032-RefSeq-gene-list-format 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532052-Jar-caching 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532092-Read-filters 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532112-Coverage-Read-depth-metrics 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532132-uBAM-Unmapped-BAM-Format 2025-12-04T17:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532152-Fisher-s-Exact-Test 2024-09-10T20:48:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532172-GATKReport-and-gsalib 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532192-Known-Issues-with-VariantRecalibrator 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532212-Deep-sequencing-data-is-missing-variants-in-M2-called-vcf 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532232-Errors-about-contigs-in-BAM-or-VCF-files-not-being-properly-ordered-or-sorted 2024-06-25T07:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD-is-lower-than-expected 2024-06-25T07:17:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532272-Missing-annotations-in-the-output-callset-VCF 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532292-missing-physical-phasing-information-in-vcf 2024-06-25T07:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532312-Errors-about-misencoded-quality-scores 2024-06-25T07:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532332-Java-version-issues 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532352-Errors-about-read-group-RG-information 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532372-Java-is-using-too-many-resources-threads-memory-or-CPU 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360035532412-Can-t-use-VQSR-on-non-model-organism-or-small-dataset 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360035535892-Somatic-copy-number-variant-discovery-CNVs 2024-06-25T07:17:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels 2024-07-24T22:47:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889451-What-input-files-does-the-GATK-accept-or-require 2024-06-25T07:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889471-How-should-I-pre-process-data-from-multiplexed-sequencing-and-multi-library-designs 2024-06-25T07:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889511-Can-I-get-a-notification-when-my-question-is-answered-or-commented-on 2024-06-25T07:17:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889531-What-are-the-requirements-for-running-GATK 2024-07-03T16:16:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889551-When-should-I-restrict-my-analysis-to-specific-intervals 2024-06-25T07:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889591-How-can-I-attend-or-host-a-GATK-workshop 2024-07-08T19:44:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889611-How-can-I-make-GATK-tools-run-faster 2024-06-25T07:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889631-Where-can-I-find-known-variants-training-and-truth-sets-and-other-resource-files 2024-06-25T07:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889691-Does-GATK-work-on-non-diploid-organisms 2024-06-25T07:15:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889711-Are-there-Best-Practices-for-calling-variants-in-RNAseq-data 2024-06-25T07:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889751-GATK-on-Amazon-Web-Services 2020-07-13T02:14:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889771-Pipelining-GATK-with-WDL-and-Cromwell 2024-06-25T07:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889791--How-to-Call-somatic-mutations-using-GATK4-Mutect2-Deprecated 2024-06-25T07:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889891--Notebook-Correlate-gCNV-callset-metrics-and-annotations 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889911--How-to-Run-the-Pathseq-pipeline 2026-02-06T20:35:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889931-Funcotator-Information-and-Tutorial 2025-09-08T16:48:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889951--How-to-Create-a-Spark-cluster-on-Google-Dataproc 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889971--How-to-Consolidate-GVCFs-for-joint-calling-with-GenotypeGVCFs 2024-06-25T07:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360035889991--How-to-Run-GATK-in-a-Docker-container 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890011--How-to-part-II-Sensitively-detect-copy-ratio-alterations-and-allelic-segments 2025-01-16T17:12:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890031--Notebook-Concordance-of-NA19017-chr20-gCNV-calls 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890411-Calling-variants-on-cohorts-of-samples-using-the-HaplotypeCaller-in-GVCF-mode 2025-03-28T14:44:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890431-The-logic-of-joint-calling-for-germline-short-variants 2024-09-04T13:21:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890451-Calculation-of-PL-and-GQ-by-HaplotypeCaller-and-GenotypeGVCFs 2024-06-25T07:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants 2024-11-06T06:35:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890491-Somatic-calling-is-NOT-simply-a-difference-between-two-callsets 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890511-Assigning-per-sample-genotypes-HaplotypeCaller 2024-06-25T07:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-BQSR 2024-08-29T20:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890551-Allele-specific-annotation-and-filtering-of-germline-short-variants 2024-06-25T07:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890571-OxoG-oxidative-artifacts 2024-06-25T07:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890591-Spark 2025-03-22T01:34:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON 2025-07-22T17:25:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890651-Version-numbers 2024-06-25T07:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups 2024-06-25T07:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies 2025-09-08T16:49:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890731-Likelihoods-and-Probabilities 2025-05-06T06:52:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890751-Jumping-libraries 2024-06-25T07:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890771-Biallelic-vs-Multiallelic-sites 2024-06-25T07:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890791-SAM-or-BAM-or-CRAM-Mapped-sequence-data-formats 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle 2026-02-19T18:48:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890831-Known-variants-Training-resources-Truth-sets 2024-06-25T07:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890851-Variant-annotations 2024-06-25T07:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890871-Heterozygosity 2024-06-25T07:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890891-Lane-Library-Sample-Cohort 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890911-Hybrid-selection-exome-preparation 2024-06-25T07:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890971-GitHub-basics-for-researchers 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035890991-PF-reads-Illumina-chastity-filter 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891011-JEXL-filtering-expressions 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891031-Mate-unmapped-records 2024-06-25T07:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891051-GenomicsDB 2026-03-16T17:47:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891071-Reference-genome 2024-06-25T07:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891091-Known-Issues-with-Mutect2-GATK4-1 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891111-Expected-variant-at-a-specific-site-was-not-called 2024-06-25T07:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891131-Errors-about-input-files-having-missing-or-incompatible-contigs 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891151-SelectVariants-Cookbook 2024-06-25T07:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891191-VariantFiltration-FT-tag 2024-06-25T07:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891211-Need-to-run-programs-that-require-different-versions-of-Java 2024-06-25T07:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360035891231-Errors-in-SAM-or-BAM-files-can-be-diagnosed-with-ValidateSamFile 2024-06-25T07:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360035894711-About-the-GATK-Best-Practices 2024-06-25T07:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels 2024-06-25T07:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036194532-What-s-in-a-GATK-workshop 2024-07-08T20:10:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036194552-Instructions-for-GATK-workshops 2024-07-08T20:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4 2024-07-20T07:59:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036227612-Local-re-assembly-and-haplotype-determination-HaplotypeCaller-and-Mutect2 2024-06-25T07:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036227632-Evaluating-the-evidence-for-haplotypes-and-variant-alleles-HaplotypeCaller-and-Mutect2 2024-06-25T07:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036227652-ActiveRegion-determination-HaplotypeCaller-and-Mutect2 2024-06-25T07:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345652-LibraryReadFilter 2019-11-23T21:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345672-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-23T21:11:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345692-NonChimericOriginalAlignmentReadFilter 2019-11-23T21:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345712-CollectHiSeqXPfFailMetrics-Picard 2019-11-23T21:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345732-GenotypeConcordance-Picard 2019-11-23T21:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345752-BwaMemIndexImageCreator 2019-11-23T21:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345772-WellformedReadFilter 2019-11-23T21:11:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345792-FirstOfPairReadFilter 2019-11-23T21:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345812-Funcotator-BETA 2019-11-23T21:11:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345832-CollectQualityYieldMetrics-Picard 2019-11-23T21:07:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345852-PathSeqPipelineSpark 2019-11-23T21:11:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345872-SecondOfPairReadFilter 2019-11-23T21:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345892-AlignmentAgreesWithHeaderReadFilter 2019-11-23T21:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345912-AS-StrandOddsRatio 2019-11-23T21:11:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345932-AnnotatePairOrientation-BETA 2019-11-23T21:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345952-FixVcfHeader-Picard 2019-11-23T21:11:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345972-CollectHsMetrics-Picard 2019-11-23T21:11:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036345992-CollectHsMetrics-Picard 2019-11-23T21:11:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346012-EstimateLibraryComplexity-Picard 2019-11-23T21:11:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346032-AllowAllReadsReadFilter 2019-11-23T21:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346052-LiftOverIntervalList-Picard 2019-11-23T21:07:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346072-VariantAnnotator-BETA 2019-11-23T21:11:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346092-FilterSamReads-Picard 2019-11-23T21:11:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346112-FilterSamReads-Picard 2019-11-23T21:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346132-PrimaryLineReadFilter 2019-11-23T21:07:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346152-CountBases 2019-11-23T21:11:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346172-StrandOddsRatio 2019-11-23T21:11:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346192--Tool-Documentation-Index 2019-12-16T20:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346212-CheckFingerprint-Picard 2019-11-23T21:07:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346232-HasReadGroupReadFilter 2019-11-23T21:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346252-DetermineGermlineContigPloidy-BETA 2019-11-23T21:07:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346272-CountVariantsSpark-BETA 2019-11-23T21:11:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346292-FisherStrand 2019-11-23T21:11:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346312-ClipReads 2019-11-23T21:11:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346332-ClipReads 2019-11-23T21:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346352-GetSampleName-BETA 2019-11-23T21:11:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346372-MarkDuplicatesSpark-BETA 2019-11-23T21:11:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346392-CalculateReadGroupChecksum-Picard 2019-11-23T21:11:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346412-SetNmMdAndUqTags-Picard 2019-11-23T21:11:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346432-CompareMetrics-Picard 2019-11-23T21:11:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346452-CompareMetrics-Picard 2019-11-23T21:11:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346472-GatherBamFiles-Picard 2019-11-23T21:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346492-GatherBamFiles-Picard 2019-11-23T21:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346512-PathSeqBuildReferenceTaxonomy 2019-11-23T21:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346532-CollectAlignmentSummaryMetrics-Picard 2019-11-23T21:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346552-AnnotateVcfWithBamDepth 2019-11-23T21:12:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346572-ExtractSequences-Picard 2019-11-23T21:12:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346592-MarkDuplicatesWithMateCigar-Picard 2019-11-23T21:12:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346612-MarkDuplicatesWithMateCigar-Picard 2019-11-23T21:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346632-CalculateContamination 2019-11-23T21:12:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346652-ApplyBQSR 2019-11-23T21:12:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346672-CpxVariantReInterpreterSpark-BETA 2019-11-23T21:12:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346692-PathSeqBuildKmers 2019-11-23T21:12:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346712-MakeSitesOnlyVcf-Picard 2019-11-23T21:12:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346732-CollectInsertSizeMetrics-Picard 2019-11-23T21:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346752-StrandBiasBySample 2019-11-23T21:12:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346772-SortSamSpark-BETA 2019-11-23T21:12:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346792-MappingQualityRankSumTest 2019-11-23T21:12:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346812-CollectJumpingLibraryMetrics-Picard 2019-11-23T21:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346832-SplitSamByNumberOfReads-Picard 2019-11-23T21:12:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346852-MateDifferentStrandReadFilter 2019-11-23T21:12:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346872-NonNFastaSize-Picard 2019-11-23T21:12:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346892-BaseRecalibratorSpark-BETA 2019-11-23T21:12:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346912-CalculateMixingFractions 2019-11-23T21:12:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346932-SelectVariants 2019-11-23T21:12:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346952-IlluminaBasecallsToSam-Picard 2019-11-23T21:12:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346972-CollectQualityYieldMetricsSpark-BETA 2019-11-23T21:12:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036346992-OxoGReadCounts 2019-11-23T21:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347012-PrintReads 2019-11-23T21:12:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347032-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-23T21:12:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347052-ValidAlignmentStartReadFilter 2019-11-23T21:12:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347072-ReadsPipelineSpark-BETA 2019-11-23T21:12:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347092-ReplaceSamHeader-Picard 2019-11-23T21:12:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347112-CountFalsePositives-BETA 2019-11-23T21:08:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347132-PolymorphicNuMT 2019-11-23T21:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347172-PathSeqBwaSpark 2019-11-23T21:12:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347192-SampleList 2019-11-23T21:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347212-MatchingBasesAndQualsReadFilter 2019-11-23T21:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347232-FragmentLength 2019-11-23T21:08:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347252-CheckIlluminaDirectory-Picard 2019-11-23T21:12:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347272-CollectBaseDistributionByCycle-Picard 2019-11-23T21:08:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347292-ReblockGVCF-EXPERIMENTAL 2019-11-23T21:12:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347312-FixMisencodedBaseQualityReads 2019-11-23T21:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347332-ModelSegments-BETA 2019-11-23T21:08:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347352-ModelSegments-BETA 2019-11-23T21:12:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347372-ExtractIlluminaBarcodes-Picard 2019-11-23T21:12:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347392-BedToIntervalList-Picard 2019-11-23T21:12:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347412-RemoveNearbyIndels 2019-11-23T21:12:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347432-FilterByOrientationBias-EXPERIMENTAL 2019-11-23T21:12:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347452-CreateSequenceDictionary-Picard 2019-11-23T21:09:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347472-PositionBasedDownsampleSam-Picard 2019-11-23T21:09:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347492-ReorderSam-Picard 2019-11-23T21:09:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347512-PostprocessGermlineCNVCalls-BETA 2019-11-23T21:12:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347532-CollectWgsMetrics-Picard 2019-11-23T21:12:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347552-LikelihoodRankSumTest 2019-11-23T21:09:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347572-RevertBaseQualityScores 2019-11-23T21:13:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347592-DownsampleSam-Picard 2019-11-23T21:13:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347612-BQSRPipelineSpark-BETA 2019-11-23T21:13:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347632-DenoiseReadCounts-BETA 2019-11-23T21:09:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347652-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-23T21:13:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347672-UpdateVcfSequenceDictionary-Picard 2019-11-23T21:09:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347692-MappingQualityZero 2019-11-23T21:13:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347712-CallCopyRatioSegments-BETA 2019-11-23T21:09:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347732-PlatformReadFilter 2019-11-23T21:09:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347752-PlotModeledSegments-BETA 2019-11-23T21:09:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347772-LiftoverVcf-Picard 2019-11-23T21:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347792-LiftoverVcf-Picard 2019-11-23T21:13:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347812-ReadPosition 2019-11-23T21:09:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347832-Coverage 2020-03-25T10:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347852-ApplyBQSRSpark-BETA 2019-11-23T21:09:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347872-CollectMultipleMetrics-Picard 2019-11-23T21:13:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347892-ValidateVariants 2019-11-23T21:13:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347912-PreprocessIntervals-BETA 2019-11-23T21:13:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347932-QualityScoreDistribution-Picard 2019-11-23T21:10:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347952-BaitDesigner-Picard 2019-11-23T21:13:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347972-InbreedingCoeff 2019-11-23T21:10:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036347992-ReadLengthEqualsCigarLengthReadFilter 2019-11-23T21:13:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348012-PrintVariantsSpark-BETA 2019-11-23T21:13:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348032-ValidateSamFile-Picard 2019-11-23T21:13:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348052-FastqToSam-Picard 2019-11-23T21:13:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348072-CollectIlluminaBasecallingMetrics-Picard 2019-11-23T21:10:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348092-FuncotatorDataSourceDownloader-BETA 2019-11-23T21:10:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348112-StrandArtifact 2019-11-23T21:10:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348132-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-23T21:10:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348152-GatherVcfsCloud-BETA 2019-11-23T21:13:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348172-PathSeqScoreSpark 2019-11-23T21:13:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348192-SplitReads 2019-11-23T21:13:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348212-AS-MappingQualityRankSumTest 2019-11-23T21:13:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348232-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-23T21:13:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348252-BaseQuality 2019-11-23T21:10:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348272-SeqIsStoredReadFilter 2019-11-23T21:10:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348292-NonZeroReferenceLengthAlignmentReadFilter 2019-11-23T21:10:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348312-CollectBaseDistributionByCycleSpark-BETA 2019-11-23T21:13:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348332-VariantRecalibrator 2019-11-23T21:13:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348352-PathSeqFilterSpark 2019-11-23T21:13:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348372-SplitIntervals 2019-11-23T21:13:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348392-UnmarkDuplicates 2019-11-23T21:13:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348412-ProperlyPairedReadFilter 2019-11-23T21:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348432-SplitVcfs-Picard 2019-11-23T21:13:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348452-GenotypeGVCFs 2019-11-23T21:14:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348472-AddCommentsToBam-Picard 2019-11-23T21:14:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348492-AS-QualByDepth 2019-11-23T21:14:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348512-Concordance-BETA 2019-11-23T21:14:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348532-FragmentLengthReadFilter 2019-11-23T21:10:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348552-BuildBamIndex-Picard 2019-11-23T21:14:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348572-NotSecondaryAlignmentReadFilter 2019-11-23T21:10:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348592-FindMendelianViolations-Picard 2019-11-23T21:14:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348612-IndexFeatureFile 2019-11-23T21:10:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348632-DepthPerSampleHC 2019-11-23T21:14:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348652-AlleleFraction 2019-11-23T21:14:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348672-RenameSampleInVcf-Picard 2019-11-23T21:14:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348692-CollectOxoGMetrics-Picard 2019-11-23T21:11:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348712-FilterVariantTranches-EXPERIMENTAL 2019-11-23T21:14:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348732-CreateSomaticPanelOfNormals-BETA 2019-11-23T21:14:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348752-CheckPileup 2019-11-23T21:14:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348832-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-23T21:29:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348852-ChromosomeCounts 2019-11-23T21:29:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348872-LibraryReadFilter 2019-11-23T21:29:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348892-NonChimericOriginalAlignmentReadFilter 2019-11-23T21:29:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348912-MeanQualityByCycle-Picard 2019-11-23T21:33:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348932-GenotypeConcordance-Picard 2019-11-23T21:33:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348952-BwaMemIndexImageCreator 2019-11-23T21:33:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348972-FirstOfPairReadFilter 2019-11-23T21:29:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036348992-CalcMetadataSpark-BETA 2019-11-23T21:33:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349012-FixVcfHeader-Picard 2019-11-23T21:33:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349032-GnarlyGenotyper-BETA 2022-06-29T11:33:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349052-EstimateLibraryComplexity-Picard 2019-11-23T21:33:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349072-ViewSam-Picard 2019-11-23T21:33:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349092-CountVariants 2019-11-23T21:33:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349112-NotDuplicateReadFilter 2019-11-23T21:29:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349132-BamToBfq-Picard 2019-11-23T21:29:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349152-VariantAnnotator-BETA 2019-11-23T21:33:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349172-PrimaryLineReadFilter 2019-11-23T21:29:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349192-StrandOddsRatio 2019-11-23T21:34:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349212--Tool-Documentation-Index 2019-12-16T20:20:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349232-HasReadGroupReadFilter 2019-11-23T21:29:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349252-DetermineGermlineContigPloidy 2019-11-23T21:29:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349272-UniqueAltReadCount 2019-11-23T21:29:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349292-MappingQuality 2019-11-23T21:29:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349312-VariantsToTable 2019-11-23T21:34:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349332-NormalizeFasta-Picard 2019-11-23T21:34:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349352-UpdateVCFSequenceDictionary 2019-11-23T21:34:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349372-IlluminaBasecallsToFastq-Picard 2019-11-23T21:34:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349392-SamFormatConverter-Picard 2019-11-23T21:30:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349412-FisherStrand 2019-11-23T21:34:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349432-ClipReads 2019-11-23T21:34:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349452-DepthPerAlleleBySample 2019-11-23T21:34:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349472-CompareMetrics-Picard 2019-11-23T21:34:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349492-FuncotateSegments-BETA 2019-11-23T21:34:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349512-GatherBamFiles-Picard 2019-11-23T21:30:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349532-CalculateFingerprintMetrics-Picard 2019-11-23T21:30:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349552-BwaSpark-BETA 2019-11-23T21:34:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349572-CalculateContamination 2019-11-23T21:34:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349592-PathSeqBuildKmers 2019-11-23T21:34:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349612-IntervalListTools-Picard 2019-11-23T21:34:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349632-SortSamSpark-BETA 2019-11-23T21:34:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349652-LeftAlignIndels 2019-11-23T21:34:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349672-MappingQualityRankSumTest 2019-11-23T21:34:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349692-MappingQualityNotZeroReadFilter 2019-11-23T21:30:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349712-HaplotypeCallerSpark-BETA 2019-11-23T21:34:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349732-NonNFastaSize-Picard 2019-11-23T21:34:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349752-CalculateMixingFractions 2019-11-23T21:34:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349772-SelectVariants 2019-11-23T21:34:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349792-MappingQualityReadFilter 2019-11-23T21:34:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349812-CollectQualityYieldMetricsSpark-BETA 2019-11-23T21:34:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349832-CreateHadoopBamSplittingIndex-BETA 2019-11-23T21:34:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349852-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-23T21:34:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349872-ReplaceSamHeader-Picard 2019-11-23T21:34:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349892-MateUnmappedAndUnmappedReadFilter 2019-11-23T21:30:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349912-CollectIlluminaLaneMetrics-Picard 2019-11-23T21:34:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349932-VcfToIntervalList-Picard 2019-11-23T21:34:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349952-SetNmAndUqTags-Picard 2019-11-23T21:34:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349972-PathSeqBwaSpark 2019-11-23T21:34:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036349992-MatchingBasesAndQualsReadFilter 2019-11-23T21:31:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350012-FragmentLength 2019-11-23T21:31:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350032-CheckIlluminaDirectory-Picard 2019-11-23T21:34:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350052-CollectTargetedPcrMetrics-Picard 2019-11-23T21:34:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350072-CollectBaseDistributionByCycle-Picard 2019-11-23T21:31:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350092-ReblockGVCF-BETA 2019-11-23T21:34:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350112-MergeBamAlignment-Picard 2019-11-23T21:31:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350132-FixMisencodedBaseQualityReads 2019-11-23T21:34:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350152-LeftAlignAndTrimVariants 2019-11-23T21:34:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350172-ModelSegments 2019-11-23T21:31:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350192-RevertSamSpark-BETA 2019-11-23T21:35:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350212-AmbiguousBaseReadFilter 2019-11-23T21:31:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350232-RemoveNearbyIndels 2019-11-23T21:35:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350252-CollectRawWgsMetrics-Picard 2019-11-23T21:35:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350272-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-23T21:35:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350292-MarkDuplicates-Picard 2019-11-23T21:35:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350312-CreateSequenceDictionary-Picard 2019-11-23T21:35:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350332-VcfToAdpc-Picard 2019-11-23T21:31:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350352-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T21:31:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350372-ReorderSam-Picard 2019-11-23T21:31:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350392-PostprocessGermlineCNVCalls 2019-11-23T21:35:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350412-CollectWgsMetrics-Picard 2019-11-23T21:35:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350432-PairedReadFilter 2019-11-23T21:31:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350452-VariantFiltration 2019-11-23T21:35:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350472-LikelihoodRankSumTest 2019-11-23T21:31:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350492-BaseRecalibrator 2019-11-23T21:35:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350512-DownsampleSam-Picard 2019-11-23T21:35:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350532-BQSRPipelineSpark-BETA 2019-11-23T21:35:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350552-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T21:35:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350572-DenoiseReadCounts 2019-11-23T21:31:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350592-BaseQualityRankSumTest 2019-11-23T21:31:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350612-IntervalListToBed-Picard 2019-11-23T21:31:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350632-ApplyVQSR 2019-11-23T21:35:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350652-MappingQualityZero 2019-11-23T21:35:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350672-ScatterIntervalsByNs-Picard 2019-11-23T21:35:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350692-BamIndexStats-Picard 2019-11-23T21:35:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350712-Mutect2 2019-11-23T21:35:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350732-AddOrReplaceReadGroups-Picard 2019-11-23T21:32:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350752-CollectVariantCallingMetrics-Picard 2019-11-23T21:32:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350792-CollectGcBiasMetrics-Picard 2019-11-23T21:32:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350812-LiftoverVcf-Picard 2019-11-23T21:35:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350832-MateOnSameContigOrNoMappedMateReadFilter 2019-11-23T21:35:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350852-ReadStrandFilter 2019-11-23T21:32:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350872-CalculateGenotypePosteriors 2019-11-23T21:35:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350892-MergeVcfs-Picard 2019-11-23T21:35:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350912-CNNScoreVariants 2019-11-23T21:35:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350932-MethylationTypeCaller-EXPERIMENTAL 2019-11-23T21:35:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350952-PreprocessIntervals 2019-11-23T21:35:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350972-QualityScoreDistribution-Picard 2019-11-23T21:32:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036350992-FlagStat 2019-11-23T21:35:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351012-BaitDesigner-Picard 2019-11-23T21:35:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351032-InbreedingCoeff 2019-11-23T21:32:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351052-ReadLengthEqualsCigarLengthReadFilter 2019-11-23T21:35:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351072-FixMateInformation-Picard 2019-11-23T21:32:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351092-SortVcf-Picard 2019-11-23T21:35:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351112-ValidateSamFile-Picard 2019-11-23T21:35:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351132-FastqToSam-Picard 2020-08-07T17:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351152-SortSam-Picard 2019-11-23T21:35:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351172-FuncotatorDataSourceDownloader 2019-11-23T21:32:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351192-MergeSamFiles-Picard 2019-11-23T21:35:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351212-GatherVcfsCloud-BETA 2019-11-23T21:35:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351232-RevertSam-Picard 2019-11-23T21:36:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351252-PassesVendorQualityCheckReadFilter 2019-11-23T21:32:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351272-AS-MappingQualityRankSumTest 2019-11-23T21:36:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351292-ReadPosRankSumTest 2019-11-23T21:32:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351312-BaseQuality 2019-11-23T21:32:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351332-SeqIsStoredReadFilter 2019-11-23T21:32:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351352-IntervalOverlapReadFilter 2019-11-23T21:32:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351372-CollectBaseDistributionByCycleSpark-BETA 2019-11-23T21:36:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351392-VariantRecalibrator 2021-04-17T13:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351412-PathSeqFilterSpark 2019-11-23T21:36:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351432-SplitIntervals 2019-11-23T21:36:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351452-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-23T21:36:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351472-SplitNCigarReads 2019-11-23T21:36:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351492-NonZeroFragmentLengthReadFilter 2019-11-23T21:32:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351512-ProperlyPairedReadFilter 2019-11-23T21:32:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351532-CigarContainsNoNOperator 2019-11-23T21:32:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351552-FilterFuncotations-EXPERIMENTAL 2019-11-23T21:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351572-SplitSamByLibrary-Picard 2019-11-23T21:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351592-CrosscheckFingerprints-Picard 2020-05-06T17:34:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351612-GenotypeGVCFs 2019-11-23T21:36:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351632-FindMendelianViolations-Picard 2019-11-23T21:36:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351652-ReferenceBases 2019-11-23T21:33:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351672-IndexFeatureFile 2019-11-23T21:33:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351692-MetricsReadFilter 2019-11-23T21:33:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351712-AlleleFraction 2019-11-23T21:36:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351732-OrientationBiasReadCounts 2019-11-23T21:33:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351752-RenameSampleInVcf-Picard 2019-11-23T21:36:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351772-MappingQualityAvailableReadFilter 2019-11-23T21:33:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351792-CountReadsSpark 2019-11-23T21:36:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351812-PrintReadsSpark 2019-11-23T21:36:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351832-ASEReadCounter 2019-11-23T21:36:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351852-CheckTerminatorBlock-Picard 2019-11-23T21:33:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036351872-CleanSam-Picard 2019-11-23T21:33:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358372-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-23T22:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358392-ChromosomeCounts 2019-11-23T22:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358412-LibraryReadFilter 2019-11-23T22:21:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358432-NonChimericOriginalAlignmentReadFilter 2019-11-23T22:21:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358452-BwaMemIndexImageCreator 2019-11-23T22:25:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358472-WellformedReadFilter 2019-11-23T22:25:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358492-SampleReadFilter 2019-11-23T22:21:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358512-AnalyzeCovariates 2019-11-23T22:25:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358532-RMSMappingQuality 2019-11-23T22:26:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358552-AlignmentAgreesWithHeaderReadFilter 2019-11-23T22:21:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358572-AS-StrandOddsRatio 2019-11-23T22:26:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358592-GnarlyGenotyper-BETA 2019-11-23T22:26:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358612-AnnotateVcfWithExpectedAlleleFraction 2019-11-23T22:26:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358632-AllowAllReadsReadFilter 2019-11-23T22:21:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358652-NotDuplicateReadFilter 2019-11-23T22:22:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358672-BamToBfq-Picard 2019-11-23T22:22:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358692-PrimaryLineReadFilter 2019-11-23T22:22:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358712-CountBases 2019-11-23T22:26:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358732-StrandOddsRatio 2019-11-23T22:26:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358752-CheckFingerprint-Picard 2019-11-23T22:22:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358772-HasReadGroupReadFilter 2019-11-23T22:22:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358792-DetermineGermlineContigPloidy 2019-11-23T22:22:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358812-FindBreakpointEvidenceSpark-BETA 2019-11-23T22:26:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358832-MappingQuality 2019-11-23T22:22:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358852-VariantsToTable 2019-11-23T22:26:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358872-AS-RMSMappingQuality 2019-11-23T22:26:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358892-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-23T22:26:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358912-CountVariantsSpark-BETA 2019-11-23T22:26:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358932-UpdateVCFSequenceDictionary 2019-11-23T22:26:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358952-SamFormatConverter-Picard 2019-11-23T22:22:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358972-MarkDuplicatesSpark 2019-11-23T22:26:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036358992-CalculateReadGroupChecksum-Picard 2019-11-23T22:26:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359012-SetNmMdAndUqTags-Picard 2019-11-23T22:26:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359032-PathSeqBuildReferenceTaxonomy 2019-11-23T22:22:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359052-AS-FisherStrand 2019-11-23T22:26:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359072-CompareBaseQualities 2019-11-23T22:22:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359092-BwaSpark-BETA 2019-11-23T22:26:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359112-CollectAlignmentSummaryMetrics-Picard 2019-11-23T22:22:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359132-AnnotateVcfWithBamDepth 2019-11-23T22:26:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359152-CollectSequencingArtifactMetrics-Picard 2019-11-23T22:22:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359172-MarkDuplicatesWithMateCigar-Picard 2019-11-23T22:26:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359192-GatherBQSRReports 2019-11-23T22:22:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359212-CalculateContamination 2019-11-23T22:26:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359232-CpxVariantReInterpreterSpark-BETA 2019-11-23T22:26:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359252-MakeSitesOnlyVcf-Picard 2019-11-23T22:26:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359272-IntervalListTools-Picard 2019-11-23T22:26:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359292-CollectInsertSizeMetrics-Picard 2019-11-23T22:22:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359312-StrandBiasBySample 2019-11-23T22:26:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359332-CollectReadCounts 2019-11-23T22:26:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359352-SortSamSpark-BETA 2019-11-23T22:26:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359372-LeftAlignIndels 2019-11-23T22:26:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359392-MappingQualityNotZeroReadFilter 2019-11-23T22:22:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359412-CollectJumpingLibraryMetrics-Picard 2019-11-23T22:22:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359432-IlluminaBasecallsToSam-Picard 2019-11-23T22:26:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359452-GenomicsDBImport 2019-11-23T22:27:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359472-CollectQualityYieldMetricsSpark-BETA 2019-11-23T22:27:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359492-CreateHadoopBamSplittingIndex-BETA 2019-11-23T22:27:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359512-PrintReads 2019-11-23T22:27:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359532-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-23T22:27:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359552-HaplotypeCaller 2019-11-23T22:27:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359572-ReadsPipelineSpark-BETA 2019-11-23T22:27:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359592-VcfToIntervalList-Picard 2019-11-23T22:27:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359612-PathSeqBwaSpark 2019-11-23T22:27:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359632-MatchingBasesAndQualsReadFilter 2019-11-23T22:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359652-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-23T22:27:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359672-FragmentLength 2019-11-23T22:23:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359692-ReblockGVCF-EXPERIMENTAL 2019-11-23T22:27:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359712-FixMisencodedBaseQualityReads 2019-11-23T22:27:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359732-ModelSegments 2019-11-23T22:23:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359752-ExtractIlluminaBarcodes-Picard 2019-11-23T22:27:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359772-AmbiguousBaseReadFilter 2019-11-23T22:23:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359792-CompareDuplicatesSpark-BETA 2019-11-23T22:27:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359812-CollectRawWgsMetrics-Picard 2019-11-23T22:27:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359832-FilterByOrientationBias-EXPERIMENTAL 2019-11-23T22:27:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359852-MarkDuplicates-Picard 2019-11-23T22:27:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359872-CreateSequenceDictionary-Picard 2019-11-23T22:27:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359892-VcfToAdpc-Picard 2019-11-23T22:23:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359912-GoodCigarReadFilter 2019-11-23T22:23:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359932-PositionBasedDownsampleSam-Picard 2019-11-23T22:23:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359952-ReorderSam-Picard 2019-11-23T22:23:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359972-GenotypeSummaries 2019-11-23T22:23:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036359992-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-23T22:27:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360012-GetPileupSummaries-BETA 2019-11-23T22:27:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360032-LikelihoodRankSumTest 2019-11-23T22:23:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360052-RevertBaseQualityScores 2019-11-23T22:27:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360072-DownsampleSam-Picard 2019-11-23T22:27:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360092-ClippingRankSumTest 2019-11-23T22:24:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360112-CompareSAMs-Picard 2019-11-23T22:27:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360132-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T22:27:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360152-CollectInsertSizeMetricsSpark-BETA 2019-11-23T22:27:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360172-BaseQualityRankSumTest 2019-11-23T22:24:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360192-ApplyVQSR 2019-11-23T22:27:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360212-ReadNameReadFilter 2019-11-23T22:24:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360232-CallCopyRatioSegments 2019-11-23T22:24:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360252-AS-InbreedingCoeff 2019-11-23T22:27:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360272-BamIndexStats-Picard 2019-11-23T22:27:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360292-FilterMutectCalls 2019-11-23T22:27:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360312-Mutect2 2019-11-23T22:27:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360332-VcfFormatConverter-Picard 2019-11-23T22:27:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360352-AddOrReplaceReadGroups-Picard 2019-11-23T22:24:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360372-CollectGcBiasMetrics-Picard 2019-11-23T22:24:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360392-ReadPosition 2019-11-23T22:24:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360412-MateOnSameContigOrNoMappedMateReadFilter 2019-11-23T22:27:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360432-Coverage 2019-11-23T22:27:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360452-ReadStrandFilter 2019-11-23T22:24:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360472-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-23T22:24:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360492-CollectMultipleMetrics-Picard 2019-11-23T22:28:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360512-CollectAllelicCounts 2019-11-23T22:28:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360532-MethylationTypeCaller-EXPERIMENTAL 2019-11-23T22:28:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360552-PreprocessIntervals 2019-11-23T22:28:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360572-QualityScoreDistribution-Picard 2019-11-23T22:24:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360592-FlagStat 2019-11-23T22:28:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360612-BaitDesigner-Picard 2019-11-23T22:28:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360632-InbreedingCoeff 2019-11-23T22:24:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360652-ReadLengthEqualsCigarLengthReadFilter 2019-11-23T22:28:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360672-PrintVariantsSpark-BETA 2019-11-23T22:28:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360692-FastqToSam-Picard 2019-11-23T22:28:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360712-ReadGroupBlackListReadFilter 2019-11-23T22:24:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360732-SamToFastq-Picard 2019-11-23T22:28:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360752-SortSam-Picard 2019-11-23T22:28:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360772-CollectIlluminaBasecallingMetrics-Picard 2019-11-23T22:24:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360792-CollectRnaSeqMetrics-Picard 2019-11-23T22:24:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360812-PassesVendorQualityCheckReadFilter 2019-11-23T22:24:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360832-AS-MappingQualityRankSumTest 2019-11-23T22:28:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360852-ReadPosRankSumTest 2019-11-23T22:25:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360872-IntervalOverlapReadFilter 2019-11-23T22:25:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360892-PathSeqFilterSpark 2019-11-23T22:28:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360912-PlotDenoisedCopyRatios 2019-11-23T22:25:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360932-FastaAlternateReferenceMaker 2019-11-23T22:28:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360952-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-23T22:28:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360972-NonZeroFragmentLengthReadFilter 2019-11-23T22:25:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036360992-CigarContainsNoNOperator 2019-11-23T22:25:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361012-SplitVcfs-Picard 2019-11-23T22:28:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361032-CrosscheckFingerprints-Picard 2019-11-23T22:28:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361052-AddCommentsToBam-Picard 2019-11-23T22:28:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361072-AS-QualByDepth 2019-11-23T22:28:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361092-AS-BaseQualityRankSumTest 2019-11-23T22:28:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361112-Concordance-BETA 2019-11-23T22:28:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361132-BuildBamIndex-Picard 2019-11-23T22:28:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361152-ReferenceBases 2019-11-23T22:25:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361172-IndexFeatureFile 2019-11-23T22:25:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361192-MetricsReadFilter 2019-11-23T22:25:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361212-FastaReferenceMaker 2019-11-23T22:28:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361232-ConvertSequencingArtifactToOxoG-Picard 2019-11-23T22:25:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361252-CountNs 2019-11-23T22:25:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361272-RenameSampleInVcf-Picard 2019-11-23T22:28:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361292-CollectOxoGMetrics-Picard 2019-11-23T22:25:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361312-PrintReadsSpark-BETA 2019-11-23T22:28:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361332-ASEReadCounter 2019-11-23T22:28:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361352-CreateSomaticPanelOfNormals-BETA 2019-11-23T22:28:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361372-CheckPileup 2019-11-23T22:28:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361392-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-23T22:31:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361412-CollectHiSeqXPfFailMetrics-Picard 2019-11-23T22:35:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361432-GenotypeConcordance-Picard 2019-11-23T22:35:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361452-Pileup 2019-11-23T22:35:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361472-OverclippedReadFilter 2019-11-23T22:31:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361492-Funcotator 2019-11-23T22:35:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361512-CollectQualityYieldMetrics-Picard 2019-11-23T22:31:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361532-CalcMetadataSpark-BETA 2019-11-23T22:35:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361552-SecondOfPairReadFilter 2019-11-23T22:31:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361572-AlignmentAgreesWithHeaderReadFilter 2019-11-23T22:31:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361592-AnnotatePairOrientation-EXPERIMENTAL 2019-11-23T22:35:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361612-FixVcfHeader-Picard 2019-11-23T22:35:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361632-GnarlyGenotyper-BETA 2019-11-23T22:35:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361652-EstimateLibraryComplexity-Picard 2019-11-23T22:36:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361672-AnnotateVcfWithExpectedAlleleFraction 2019-11-23T22:36:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361692-CountVariants 2019-11-23T22:36:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361712-NotDuplicateReadFilter 2019-11-23T22:31:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361732-BamToBfq-Picard 2019-11-23T22:31:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361752-VariantAnnotator-BETA 2019-11-23T22:36:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361772-StrandOddsRatio 2021-06-24T17:29:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361792-DetermineGermlineContigPloidy 2019-11-23T22:32:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361812-FindBreakpointEvidenceSpark-BETA 2019-11-23T22:36:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361832-UniqueAltReadCount 2019-11-23T22:32:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361852-MappingQuality 2019-11-23T22:32:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361872-VariantsToTable 2019-11-23T22:36:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361892-NormalizeFasta-Picard 2019-11-23T22:36:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361912-AS-RMSMappingQuality 2019-11-23T22:36:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361932-CountVariantsSpark-BETA 2019-11-23T22:36:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361952-UpdateVCFSequenceDictionary 2019-11-23T22:36:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361972-IlluminaBasecallsToFastq-Picard 2019-11-23T22:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036361992-FisherStrand 2019-11-23T22:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362012-CollectSamErrorMetrics-Picard 2019-11-23T22:32:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362032-GetSampleName-BETA 2019-11-23T22:36:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362052-MarkDuplicatesSpark 2019-11-23T22:36:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362072-DepthPerAlleleBySample 2019-11-23T22:36:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362092-SetNmMdAndUqTags-Picard 2019-11-23T22:36:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362112-GatherBamFiles-Picard 2019-11-23T22:32:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362132-CalculateFingerprintMetrics-Picard 2019-11-23T22:32:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362152-PathSeqBuildReferenceTaxonomy 2019-11-23T22:32:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362172-CompareBaseQualities 2019-11-23T22:32:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362192-CollectAlignmentSummaryMetrics-Picard 2019-11-23T22:32:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362212-MappedReadFilter 2019-11-23T22:32:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362232-ExtractSequences-Picard 2019-11-23T22:36:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362252-MarkDuplicatesWithMateCigar-Picard 2019-11-23T22:36:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362272-GatherBQSRReports 2019-11-23T22:32:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362292-ApplyBQSR 2019-11-23T22:36:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362312-CpxVariantReInterpreterSpark-BETA 2019-11-23T22:36:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362332-StrandBiasBySample 2019-11-23T22:36:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362352-LeftAlignIndels 2019-11-23T22:36:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362372-FilterIntervals 2019-11-23T22:32:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362392-MappingQualityRankSumTest 2019-11-23T22:36:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362412-CollectJumpingLibraryMetrics-Picard 2019-11-23T22:32:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362432-SplitSamByNumberOfReads-Picard 2019-11-23T22:36:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362452-MateDifferentStrandReadFilter 2019-11-23T22:36:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362472-NonNFastaSize-Picard 2019-11-23T22:36:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362492-FilterMutectCalls 2019-11-23T22:36:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362512-CalculateMixingFractions 2019-11-23T22:36:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362532-SelectVariants 2022-04-13T00:41:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362552-ReadGroupReadFilter 2019-11-23T22:32:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362572-MappingQualityReadFilter 2019-11-23T22:36:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362592-CollectQualityYieldMetricsSpark-BETA 2019-11-23T22:36:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362612-OxoGReadCounts 2019-11-23T22:33:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362632-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-23T22:36:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362652-CrosscheckReadGroupFingerprints-Picard 2019-11-23T22:33:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362672-HaplotypeCaller 2019-11-23T22:36:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362692-ValidAlignmentStartReadFilter 2019-11-23T22:36:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362712-ReplaceSamHeader-Picard 2019-11-23T22:36:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362732-MateUnmappedAndUnmappedReadFilter 2019-11-23T22:33:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362752-CollectIlluminaLaneMetrics-Picard 2019-11-23T22:36:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362772-CountBasesInReference 2019-11-23T22:36:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362792-SetNmAndUqTags-Picard 2019-11-23T22:36:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362812-SampleList 2019-11-23T22:33:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362832-FragmentLength 2019-11-23T22:33:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362852-CheckIlluminaDirectory-Picard 2019-11-23T22:37:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362872-CollectBaseDistributionByCycle-Picard 2019-11-23T22:33:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362892-MergeBamAlignment-Picard 2019-11-23T22:33:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362912-RevertSamSpark-BETA 2019-11-23T22:37:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362932-BedToIntervalList-Picard 2019-11-23T22:37:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362952-RemoveNearbyIndels 2019-11-23T22:37:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362972-CompareDuplicatesSpark-BETA 2019-11-23T22:37:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036362992-FilterByOrientationBias-EXPERIMENTAL 2019-11-23T22:37:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363012-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-23T22:37:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363032-OriginalAlignment 2019-11-23T22:33:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363052-VcfToAdpc-Picard 2019-11-23T22:33:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363092-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T22:33:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363192-PostprocessGermlineCNVCalls 2019-11-23T22:37:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363212-NotSupplementaryAlignmentReadFilter 2019-11-23T22:33:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363232-GenotypeSummaries 2019-11-23T22:33:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363252-CollectWgsMetrics-Picard 2019-11-23T22:37:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363272-AS-ReadPosRankSumTest 2019-11-23T22:37:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363292-GetPileupSummaries-BETA 2019-11-23T22:37:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363312-ExcessHet 2019-11-23T22:33:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363332-BaseRecalibrator 2019-11-23T22:37:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363352-DownsampleSam-Picard 2019-11-23T22:37:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363372-CompareSAMs-Picard 2019-11-23T22:37:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363392-PossibleDeNovo 2019-11-23T22:33:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363412-CollectInsertSizeMetricsSpark-BETA 2019-11-23T22:37:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363432-DenoiseReadCounts 2019-11-23T22:33:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363452-GermlineCNVCaller 2019-11-23T22:34:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363472-UpdateVcfSequenceDictionary-Picard 2019-11-23T22:34:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363492-MappingQualityZero 2019-11-23T22:37:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363512-PlatformReadFilter 2019-11-23T22:34:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363532-VcfFormatConverter-Picard 2019-11-23T22:37:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363552-AddOrReplaceReadGroups-Picard 2019-11-23T22:34:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363572-PlotModeledSegments 2019-11-23T22:34:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363592-CollectVariantCallingMetrics-Picard 2019-11-23T22:34:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363612-CombineGVCFs 2019-11-23T22:37:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363632-LiftoverVcf-Picard 2019-11-23T22:37:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363652-AddOATag-Picard 2019-11-23T22:37:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363672-ApplyBQSRSpark-BETA 2019-11-23T22:37:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363692-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-23T22:34:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363712-MergeVcfs-Picard 2019-11-23T22:37:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363732-CollectMultipleMetrics-Picard 2019-11-23T22:37:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363752-CollectAllelicCounts 2019-11-23T22:37:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363772-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-23T22:34:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363792-PreprocessIntervals 2019-11-23T22:37:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363812-BaitDesigner-Picard 2019-11-23T22:37:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363832-ValidateSamFile-Picard 2019-11-23T22:37:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363852-FastqToSam-Picard 2019-11-23T22:37:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363872-ReadGroupBlackListReadFilter 2019-11-23T22:34:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363892-StrandArtifact 2019-11-23T22:34:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363912-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-23T22:34:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363932-CollectRnaSeqMetrics-Picard 2019-11-23T22:34:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363952-PathSeqScoreSpark 2019-11-23T22:38:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363972-RevertSam-Picard 2019-11-23T22:38:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036363992-PassesVendorQualityCheckReadFilter 2019-11-23T22:34:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364012-SplitReads 2019-11-23T22:38:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364032-AS-MappingQualityRankSumTest 2019-11-23T22:38:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364052-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-23T22:38:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364072-SeqIsStoredReadFilter 2019-11-23T22:34:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364092-IntervalOverlapReadFilter 2019-11-23T22:34:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364112-PathSeqFilterSpark 2019-11-23T22:38:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364132-PlotDenoisedCopyRatios 2019-11-23T22:34:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364152-SplitIntervals 2019-11-23T22:38:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364172-UnmarkDuplicates 2019-11-23T22:38:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364192-EvaluateInfoFieldConcordance-BETA 2019-11-23T22:38:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364212-SplitVcfs-Picard 2019-11-23T22:38:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364232-CrosscheckFingerprints-Picard 2019-11-23T22:38:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364252-CNNVariantTrain-EXPERIMENTAL 2019-11-23T22:38:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364272-TandemRepeat 2019-11-23T22:35:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364292-AddCommentsToBam-Picard 2019-11-23T22:38:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364312-AnalyzeSaturationMutagenesis-BETA 2019-11-23T22:38:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364332-AS-BaseQualityRankSumTest 2019-11-23T22:38:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364352-NotSecondaryAlignmentReadFilter 2019-11-23T22:35:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364372-IndexFeatureFile 2019-11-23T22:35:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364392-DepthPerSampleHC 2019-11-23T22:38:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364412-AlleleFraction 2019-11-23T22:38:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364432-ConvertSequencingArtifactToOxoG-Picard 2019-11-23T22:35:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364452-MappingQualityAvailableReadFilter 2019-11-23T22:35:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364472-CountBasesSpark-BETA 2019-11-23T22:38:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364492-PrintReadsSpark-BETA 2019-11-23T22:38:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364512-FilterVariantTranches 2019-11-23T22:38:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364532-CreateSomaticPanelOfNormals-BETA 2019-11-23T22:38:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364552-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-23T22:44:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364572-ChromosomeCounts 2019-11-23T22:44:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364592-LibraryReadFilter 2019-11-23T22:44:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364612-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-23T22:48:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364632-MeanQualityByCycle-Picard 2019-11-23T22:48:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364652-Pileup 2023-03-09T16:40:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364672-OverclippedReadFilter 2019-11-23T22:44:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364692-BwaMemIndexImageCreator 2019-11-23T22:48:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364712-RMSMappingQuality 2019-11-23T22:48:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364732-FirstOfPairReadFilter 2019-11-23T22:44:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364752-Funcotator 2019-11-23T22:48:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364772-CollectQualityYieldMetrics-Picard 2019-11-23T22:44:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364792-PathSeqPipelineSpark 2019-11-23T22:48:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364812-CalcMetadataSpark-BETA 2019-11-23T22:48:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364832-SecondOfPairReadFilter 2019-11-23T22:44:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364852-AS-StrandOddsRatio 2019-11-23T22:48:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364872-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-23T22:48:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364892-AnnotatePairOrientation-EXPERIMENTAL 2019-11-23T22:48:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364912-VariantEval-BETA 2019-11-23T22:48:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364932-FixVcfHeader-Picard 2019-11-23T22:48:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364952-AnnotateVcfWithExpectedAlleleFraction 2019-11-23T22:48:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364972-CountVariants 2019-11-23T22:48:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036364992-LiftOverIntervalList-Picard 2019-11-23T22:44:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365012-BamToBfq-Picard 2019-11-23T22:44:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365032-VariantAnnotator-BETA 2019-11-23T22:48:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365052-FilterSamReads-Picard 2019-11-23T22:48:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365072-CollectMultipleMetricsSpark-BETA 2019-11-23T22:48:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365092--Tool-Documentation-Index 2019-12-16T20:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365112-CheckFingerprint-Picard 2019-11-23T22:44:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365132-FindBreakpointEvidenceSpark-BETA 2019-11-23T22:48:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365152-UniqueAltReadCount 2019-11-23T22:44:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365172-QualByDepth 2019-11-23T22:48:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365192-NormalizeFasta-Picard 2019-11-23T22:48:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365212-AS-RMSMappingQuality 2019-11-23T22:48:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365232-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-23T22:48:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365252-SamFormatConverter-Picard 2019-11-23T22:44:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365272-CollectSamErrorMetrics-Picard 2019-11-23T22:44:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365292-GetSampleName-BETA 2019-11-23T22:48:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365312-MarkDuplicatesSpark 2019-11-23T22:48:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365332-PathSeqBuildReferenceTaxonomy 2019-11-23T22:45:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365352-CompareBaseQualities 2019-11-23T22:45:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365372-CollectAlignmentSummaryMetrics-Picard 2019-11-23T22:45:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365392-AnnotateVcfWithBamDepth 2019-11-23T22:48:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365412-CollectSequencingArtifactMetrics-Picard 2019-11-23T22:45:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365432-GatherVcfs-Picard 2019-11-23T22:45:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365452-ExtractSequences-Picard 2019-11-23T22:48:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365472-GatherBQSRReports 2019-11-23T22:45:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365492-ApplyBQSR 2019-11-23T22:49:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365512-CpxVariantReInterpreterSpark-BETA 2019-11-23T22:49:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365532-PathSeqBuildKmers 2019-11-23T22:49:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365552-IntervalListTools-Picard 2019-11-23T22:49:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365572-CollectInsertSizeMetrics-Picard 2019-11-23T22:45:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365592-StrandBiasBySample 2019-11-23T22:49:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365612-SortSamSpark-BETA 2019-11-23T22:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365632-LeftAlignIndels 2019-11-23T22:49:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365652-FilterIntervals 2019-11-23T22:45:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365672-MappingQualityRankSumTest 2019-11-23T22:49:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365692-MappingQualityNotZeroReadFilter 2019-11-23T22:45:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365712-CollectJumpingLibraryMetrics-Picard 2019-11-23T22:45:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365732-MateDifferentStrandReadFilter 2019-11-23T22:49:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365752-SelectVariants 2019-11-23T22:49:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365772-ReadGroupReadFilter 2019-11-23T22:45:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365792-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-23T22:49:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365812-HaplotypeCaller 2019-11-23T22:49:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365832-ValidAlignmentStartReadFilter 2019-11-23T22:49:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365852-ReadsPipelineSpark-BETA 2019-11-23T22:49:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365872-ReplaceSamHeader-Picard 2019-11-23T22:49:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365892-CountFalsePositives-BETA 2019-11-23T22:49:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365912-MateUnmappedAndUnmappedReadFilter 2019-11-23T22:45:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365932-VcfToIntervalList-Picard 2019-11-23T22:49:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365952-SetNmAndUqTags-Picard 2019-11-23T22:49:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365972-PathSeqBwaSpark 2019-11-23T22:49:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036365992-MarkIlluminaAdapters-Picard 2019-11-23T22:49:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366012-MatchingBasesAndQualsReadFilter 2019-11-23T22:45:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366032-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-23T22:49:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366052-MeanQualityByCycleSpark-BETA 2019-11-23T22:49:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366072-ReblockGVCF-EXPERIMENTAL 2019-11-23T22:49:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366092-FixMisencodedBaseQualityReads 2019-11-23T22:49:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366112-LeftAlignAndTrimVariants 2019-11-23T22:49:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366132-AmbiguousBaseReadFilter 2019-11-23T22:46:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366152-RemoveNearbyIndels 2019-11-23T22:49:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366172-OriginalAlignment 2019-11-23T22:46:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366192-MarkDuplicates-Picard 2019-11-23T22:49:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366212-CreateSequenceDictionary-Picard 2019-11-23T22:49:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366232-VcfToAdpc-Picard 2019-11-23T22:46:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366252-PositionBasedDownsampleSam-Picard 2019-11-23T22:46:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366272-ReorderSam-Picard 2019-11-23T22:46:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366292-PostprocessGermlineCNVCalls 2019-11-23T22:49:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366312-NotSupplementaryAlignmentReadFilter 2019-11-23T22:46:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366332-GetPileupSummaries-BETA 2019-11-23T22:49:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366352-LikelihoodRankSumTest 2019-11-23T22:46:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366372-DownsampleSam-Picard 2019-11-23T22:49:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366392-BQSRPipelineSpark-BETA 2019-11-23T22:49:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366412-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T22:49:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366432-PossibleDeNovo 2019-11-23T22:46:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366452-CollectInsertSizeMetricsSpark-BETA 2019-11-23T22:49:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366472-BaseQualityRankSumTest 2019-11-23T22:46:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366492-IntervalListToBed-Picard 2019-11-23T22:46:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366512-ApplyVQSR 2019-11-23T22:50:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366532-GermlineCNVCaller 2019-11-23T22:46:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366552-FilterMutectCalls 2019-11-23T22:50:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366572-VcfFormatConverter-Picard 2019-11-23T22:50:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366592-CollectVariantCallingMetrics-Picard 2019-11-23T22:46:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366612-CombineGVCFs 2019-11-23T22:50:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366632-AddOATag-Picard 2019-11-23T22:50:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366652-ReadPosition 2019-11-23T22:46:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366672-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-23T22:46:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366692-MergeVcfs-Picard 2019-11-23T22:50:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366712-CollectMultipleMetrics-Picard 2019-11-23T22:50:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366732-CollectAllelicCounts 2019-11-23T22:50:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366752-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-23T22:47:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366792-MethylationTypeCaller-EXPERIMENTAL 2019-11-23T22:50:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366812-FlagStat 2019-11-23T22:50:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366832-BaitDesigner-Picard 2019-11-23T22:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366852-InbreedingCoeff 2019-11-23T22:47:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366872-PrintVariantsSpark-BETA 2019-11-23T22:50:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366892-ValidateSamFile-Picard 2019-11-23T22:50:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366912-ReadGroupBlackListReadFilter 2019-11-23T22:47:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366932-SortSam-Picard 2019-11-23T22:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366952-CollectIlluminaBasecallingMetrics-Picard 2019-11-23T22:47:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366972-StrandArtifact 2019-11-23T22:47:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036366992-GatherVcfsCloud-BETA 2019-11-23T22:50:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367012-PassesVendorQualityCheckReadFilter 2019-11-23T22:47:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367032-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-23T22:50:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367052-ReadPosRankSumTest 2019-11-23T22:47:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367072-SeqIsStoredReadFilter 2019-11-23T22:47:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367092-CollectBaseDistributionByCycleSpark-BETA 2019-11-23T22:50:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367112-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-23T22:50:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367132-PlotDenoisedCopyRatios 2019-11-23T22:47:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367152-SplitIntervals 2019-11-23T22:50:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367172-FastaAlternateReferenceMaker 2019-11-23T22:50:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367192-UnmarkDuplicates 2019-11-23T22:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367212-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-23T22:50:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367232-NonZeroFragmentLengthReadFilter 2019-11-23T22:47:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367252-FilterFuncotations-EXPERIMENTAL 2019-11-23T22:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367272-TandemRepeat 2019-11-23T22:47:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367292-FindBadGenomicKmersSpark-BETA 2019-11-23T22:50:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367312-AnalyzeSaturationMutagenesis-BETA 2019-11-23T22:50:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367332-AS-QualByDepth 2019-11-23T22:50:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367352-AS-BaseQualityRankSumTest 2019-11-23T22:51:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367372-FragmentLengthReadFilter 2019-11-23T22:47:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367392-FindMendelianViolations-Picard 2019-11-23T22:51:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367412-IndexFeatureFile 2019-11-23T22:47:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367432-MetricsReadFilter 2019-11-23T22:47:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367452-FastaReferenceMaker 2019-11-23T22:51:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367472-QualityScoreDistributionSpark-BETA 2019-11-23T22:51:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367492-DepthPerSampleHC 2019-11-23T22:51:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367512-AlleleFraction 2019-11-23T22:51:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367532-ConvertSequencingArtifactToOxoG-Picard 2019-11-23T22:48:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367552-OrientationBiasReadCounts 2019-11-23T22:48:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367572-RenameSampleInVcf-Picard 2019-11-23T22:51:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367592-MappingQualityAvailableReadFilter 2019-11-23T22:48:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367612-CreateReadCountPanelOfNormals 2019-11-23T22:48:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367632-CountBasesSpark-BETA 2019-11-23T22:51:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367652-PrintReadsSpark-BETA 2019-11-23T22:51:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367672-FilterVariantTranches 2019-11-23T22:51:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367692-CreateSomaticPanelOfNormals-BETA 2019-11-23T22:51:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367712-GtcToVcf-Picard 2019-11-23T22:48:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036367732-CheckTerminatorBlock-Picard 2019-11-23T22:48:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429352-LibraryReadFilter 2019-11-25T15:43:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429372-NonChimericOriginalAlignmentReadFilter 2019-11-25T15:43:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429392-MeanQualityByCycle-Picard 2019-11-25T15:48:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429432-GenotypeConcordance-Picard 2019-11-25T15:48:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429452-Pileup 2019-11-25T15:48:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429472-WellformedReadFilter 2019-11-25T15:48:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429492-AnalyzeCovariates 2019-11-25T15:48:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429512-FirstOfPairReadFilter 2019-11-25T15:43:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429532-PathSeqPipelineSpark 2019-11-25T15:48:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429552-FilterVcf-Picard 2019-11-25T15:44:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429572-EstimateLibraryComplexity-Picard 2019-11-25T15:48:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429612-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T15:48:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429652-NotDuplicateReadFilter 2019-11-25T15:44:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429672-VariantAnnotator-BETA 2019-11-25T15:48:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429692-FilterSamReads-Picard 2019-11-25T15:48:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429712-CountBases 2019-11-25T15:48:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429732-StrandOddsRatio 2019-11-25T15:48:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429752--Tool-Documentation-Index 2019-12-16T20:20:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429772-CheckFingerprint-Picard 2019-11-25T15:44:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429792-HasReadGroupReadFilter 2019-11-25T15:44:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429812-DetermineGermlineContigPloidy-BETA 2019-11-25T15:44:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429832-MappingQuality 2019-11-25T15:44:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429852-VariantsToTable 2019-11-25T15:48:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429872-AS-RMSMappingQuality 2019-11-25T15:48:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429892-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T15:48:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429912-CountVariantsSpark-BETA 2019-11-25T15:48:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429932-UpdateVCFSequenceDictionary 2019-11-25T15:48:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429952-ClipReads 2019-11-25T15:48:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429972-CollectSamErrorMetrics-Picard 2019-11-25T15:44:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036429992-CompareMetrics-Picard 2019-11-25T15:48:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430012-GatherBamFiles-Picard 2019-11-25T15:44:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430032-CalculateFingerprintMetrics-Picard 2019-11-25T15:44:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430052-PathSeqBuildReferenceTaxonomy 2019-11-25T15:44:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430072-BwaSpark-BETA 2019-11-25T15:48:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430092-AnnotateVcfWithBamDepth 2019-11-25T15:48:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430112-GatherVcfs-Picard 2019-11-25T15:44:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430132-ExtractSequences-Picard 2019-11-25T15:48:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430152-CalculateContamination 2019-11-25T15:48:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430172-PathSeqBuildKmers 2019-11-25T15:48:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430192-IntervalListTools-Picard 2019-11-25T15:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430212-StrandBiasBySample 2019-11-25T15:48:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430232-CollectReadCounts-BETA 2019-11-25T15:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430252-SortSamSpark-BETA 2019-11-25T15:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430272-LeftAlignIndels 2019-11-25T15:48:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430292-FilterIntervals 2019-11-25T15:45:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430312-HaplotypeCallerSpark-BETA 2019-11-25T15:48:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430332-CollectJumpingLibraryMetrics-Picard 2019-11-25T15:45:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430352-SplitSamByNumberOfReads-Picard 2019-11-25T15:48:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430372-MateDifferentStrandReadFilter 2019-11-25T15:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430392-FilterMutectCalls 2019-11-25T15:48:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430412-BaseRecalibratorSpark-BETA 2019-11-25T15:48:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430432-SelectVariants 2019-11-25T15:48:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430452-AccumulateVariantCallingMetrics-Picard 2019-11-25T15:45:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430472-IlluminaBasecallsToSam-Picard 2019-11-25T15:49:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430492-ReadGroupReadFilter 2019-11-25T15:45:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430512-MappingQualityReadFilter 2019-11-25T15:49:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430532-GenomicsDBImport 2019-11-25T15:49:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430552-PlatformUnitReadFilter 2019-11-25T15:45:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430572-OxoGReadCounts 2019-11-25T15:45:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430592-CrosscheckReadGroupFingerprints-Picard 2019-11-25T15:45:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430612-ValidAlignmentStartReadFilter 2019-11-25T15:49:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430632-ReadsPipelineSpark-BETA 2019-11-25T15:49:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430652-ReplaceSamHeader-Picard 2019-11-25T15:49:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430672-CountFalsePositives-BETA 2019-11-25T15:49:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430692-PolymorphicNuMT 2019-11-25T15:45:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430712-VcfToIntervalList-Picard 2019-11-25T15:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430732-SetNmAndUqTags-Picard 2019-11-25T15:49:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430752-PathSeqBwaSpark 2019-11-25T15:49:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430772-MatchingBasesAndQualsReadFilter 2019-11-25T15:45:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430792-MeanQualityByCycleSpark-BETA 2019-11-25T15:49:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430812-CheckIlluminaDirectory-Picard 2019-11-25T15:49:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430832-CollectBaseDistributionByCycle-Picard 2019-11-25T15:45:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430872-FixMisencodedBaseQualityReads 2019-11-25T15:49:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430892-RevertSamSpark-BETA 2019-11-25T15:49:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430912-BedToIntervalList-Picard 2019-11-25T15:49:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430932-RemoveNearbyIndels 2019-11-25T15:49:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430972-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T15:49:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036430992-OriginalAlignment 2019-11-25T15:45:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431012-CreateSequenceDictionary-Picard 2019-11-25T15:49:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431032-VcfToAdpc-Picard 2019-11-25T15:45:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431052-GoodCigarReadFilter 2019-11-25T15:45:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431072-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T15:45:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431092-PositionBasedDownsampleSam-Picard 2019-11-25T15:45:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431112-ReorderSam-Picard 2019-11-25T15:45:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431132-PostprocessGermlineCNVCalls-BETA 2019-11-25T15:49:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431152-NotSupplementaryAlignmentReadFilter 2019-11-25T15:45:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431172-FlagStatSpark-BETA 2019-11-25T15:49:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431212-PairedReadFilter 2019-11-25T15:46:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431232-AS-ReadPosRankSumTest 2019-11-25T15:49:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431252-ExcessHet 2019-11-25T15:46:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431272-GatherTranches-BETA 2019-11-25T15:46:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431292-DownsampleSam-Picard 2019-11-25T15:49:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431312-EstimateLibraryComplexityGATK-BETA 2019-11-25T15:46:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431332-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T15:49:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431352-CollectInsertSizeMetricsSpark-BETA 2019-11-25T15:49:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431372-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T15:49:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431392-ApplyVQSR 2019-11-25T15:49:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431412-UpdateVcfSequenceDictionary-Picard 2019-11-25T15:46:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431432-ReadNameReadFilter 2019-11-25T15:46:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431452-MappingQualityZero 2019-11-25T15:49:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431472-ScatterIntervalsByNs-Picard 2019-11-25T15:49:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431492-Mutect2 2019-11-25T15:49:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431512-PlotModeledSegments-BETA 2019-11-25T15:46:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431532-LiftoverVcf-Picard 2019-11-25T15:49:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431552-AddOATag-Picard 2019-11-25T15:49:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431572-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T15:50:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431592-ReadStrandFilter 2019-11-25T15:46:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431612-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T15:46:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431632-CalculateGenotypePosteriors 2019-11-25T15:50:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431652-MergeVcfs-Picard 2019-11-25T15:50:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431672-CollectMultipleMetrics-Picard 2019-11-25T15:50:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431692-ValidateVariants 2019-11-25T15:50:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431712-ExtractSVEvidenceSpark-BETA 2019-11-25T15:50:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431732-CollectAllelicCounts-BETA 2019-11-25T15:50:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431752-CNNScoreVariants-EXPERIMENTAL 2019-11-25T15:50:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431772-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T15:46:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431792-FlagStat 2019-11-25T15:50:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431812-BaitDesigner-Picard 2019-11-25T15:50:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431832-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T15:50:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431852-SortVcf-Picard 2019-11-25T15:50:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431872-FastqToSam-Picard 2019-11-25T15:50:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431892-ReadGroupBlackListReadFilter 2019-11-25T15:46:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431912-SamToFastq-Picard 2019-11-25T15:50:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431932-SortSam-Picard 2019-11-25T15:50:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431952-StrandArtifact 2019-11-25T15:46:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431972-AnnotateIntervals-BETA 2019-11-25T15:50:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036431992-RevertSam-Picard 2019-11-25T15:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432012-PassesVendorQualityCheckReadFilter 2019-11-25T15:47:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432052-AS-MappingQualityRankSumTest 2019-11-25T15:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432072-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T15:50:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432092-ReadPosRankSumTest 2019-11-25T15:47:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432112-BaseQuality 2019-11-25T15:47:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432132-SeqIsStoredReadFilter 2019-11-25T15:47:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432172-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T15:50:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432192-PlotDenoisedCopyRatios-BETA 2019-11-25T15:47:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432212-UnmarkDuplicates 2019-11-25T15:50:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432232-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T15:50:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432252-SplitNCigarReads 2019-11-25T15:50:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432272-PileupSpark-BETA 2019-11-25T15:50:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432292-CigarContainsNoNOperator 2019-11-25T15:47:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432312-SplitVcfs-Picard 2019-11-25T15:50:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432332-FilterFuncotations-EXPERIMENTAL 2019-11-25T15:50:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432352-SplitSamByLibrary-Picard 2019-11-25T15:50:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432372-CrosscheckFingerprints-Picard 2019-11-25T15:50:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432392-GenotypeGVCFs 2019-11-25T15:50:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432412-AS-QualByDepth 2019-11-25T15:50:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432432-BuildBamIndex-Picard 2019-11-25T15:50:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432452-CollectRrbsMetrics-Picard 2019-11-25T15:47:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432472-ReferenceBases 2019-11-25T15:47:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432492-QualityScoreDistributionSpark-BETA 2019-11-25T15:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432512-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T15:47:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432532-CountBasesSpark-BETA 2019-11-25T15:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432552-ASEReadCounter 2020-02-27T19:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432572-CreateSomaticPanelOfNormals-BETA 2019-11-25T15:50:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432592-CheckPileup 2019-11-25T15:50:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432612-GtcToVcf-Picard 2019-11-25T15:47:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432632-CleanSam-Picard 2019-11-25T15:47:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432732-ChromosomeCounts 2019-11-25T15:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432752-LibraryReadFilter 2019-11-25T15:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432772-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T15:57:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432792-OverclippedReadFilter 2019-11-25T15:52:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432812-BwaMemIndexImageCreator 2019-11-25T15:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432832-RMSMappingQuality 2019-11-25T15:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432852-Funcotator-BETA 2019-11-25T15:57:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432872-CalcMetadataSpark-BETA 2019-11-25T15:57:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432892-SecondOfPairReadFilter 2019-11-25T15:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432912-FilterVcf-Picard 2019-11-25T15:53:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432932-CountReads 2019-11-25T15:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432952-FixVcfHeader-Picard 2019-11-25T15:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432972-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T15:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036432992-CountVariants 2019-11-25T15:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433012-NotDuplicateReadFilter 2019-11-25T15:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433032-VariantAnnotator-BETA 2019-11-25T15:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433052-FilterSamReads-Picard 2019-11-25T15:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433072-PrimaryLineReadFilter 2019-11-25T15:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433092-CountBases 2019-11-25T15:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433112-StrandOddsRatio 2019-11-25T15:57:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433132--Tool-Documentation-Index 2019-12-16T20:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433152-CheckFingerprint-Picard 2019-11-25T15:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433172-HasReadGroupReadFilter 2019-11-25T15:53:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433192-DetermineGermlineContigPloidy-BETA 2019-11-25T15:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433212-FindBreakpointEvidenceSpark-BETA 2019-11-25T15:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433232-UniqueAltReadCount 2019-11-25T15:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433252-MappingQuality 2019-11-25T15:53:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433272-QualByDepth 2019-11-25T15:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433292-VariantsToTable 2019-11-25T15:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433312-AS-RMSMappingQuality 2019-11-25T15:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433332-CountVariantsSpark-BETA 2019-11-25T15:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433352-IlluminaBasecallsToFastq-Picard 2019-11-25T15:57:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433372-SamFormatConverter-Picard 2019-11-25T15:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433392-SoftClippedReadFilter 2019-11-25T15:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433412-GetSampleName-BETA 2019-11-25T15:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433432-DepthPerAlleleBySample 2019-11-25T15:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433452-CalculateReadGroupChecksum-Picard 2019-11-25T15:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433472-CompareMetrics-Picard 2019-11-25T15:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433492-FuncotateSegments-BETA 2019-11-25T15:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433512-GatherBamFiles-Picard 2019-11-25T15:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433532-AS-FisherStrand 2019-11-25T15:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433552-AnnotateVcfWithBamDepth 2019-11-25T15:57:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433572-MappedReadFilter 2019-11-25T15:53:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433592-ExtractSequences-Picard 2019-11-25T15:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433612-MarkDuplicatesWithMateCigar-Picard 2019-11-25T15:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433632-CalculateContamination 2019-11-25T15:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433652-ApplyBQSR 2019-11-25T15:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433692-CpxVariantReInterpreterSpark-BETA 2019-11-25T15:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433712-IntervalListTools-Picard 2019-11-25T15:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433732-CollectInsertSizeMetrics-Picard 2019-11-25T15:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433752-StrandBiasBySample 2019-11-25T15:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433772-SortSamSpark-BETA 2019-11-25T15:58:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433792-LeftAlignIndels 2019-11-25T15:58:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433812-FilterIntervals 2019-11-25T15:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433832-HaplotypeCallerSpark-BETA 2019-11-25T15:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433852-FilterMutectCalls 2019-11-25T15:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433872-BaseRecalibratorSpark-BETA 2019-11-25T15:58:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433892-CalculateMixingFractions 2019-11-25T15:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433912-SelectVariants 2019-11-25T15:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433932-AccumulateVariantCallingMetrics-Picard 2019-11-25T15:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433952-IlluminaBasecallsToSam-Picard 2019-11-25T15:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433972-ReadGroupReadFilter 2019-11-25T15:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036433992-MappingQualityReadFilter 2019-11-25T15:58:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434012-CollectQualityYieldMetricsSpark-BETA 2019-11-25T15:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434032-PlatformUnitReadFilter 2019-11-25T15:54:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434052-PrintReads 2019-11-25T15:58:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434072-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T15:58:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434092-ValidAlignmentStartReadFilter 2019-11-25T15:58:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434112-CollectIlluminaLaneMetrics-Picard 2019-11-25T15:58:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434132-PolymorphicNuMT 2019-11-25T15:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434152-VcfToIntervalList-Picard 2019-11-25T15:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434172-SampleList 2019-11-25T15:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434192-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T15:58:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434212-MeanQualityByCycleSpark-BETA 2019-11-25T15:58:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434232-CollectTargetedPcrMetrics-Picard 2019-11-25T15:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434252-FixMisencodedBaseQualityReads 2019-11-25T15:58:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434272-RevertSamSpark-BETA 2019-11-25T15:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434292-AmbiguousBaseReadFilter 2019-11-25T15:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434312-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T15:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434332-OriginalAlignment 2019-11-25T15:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434352-CreateSequenceDictionary-Picard 2019-11-25T15:58:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434372-ReorderSam-Picard 2019-11-25T15:55:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434392-NotSupplementaryAlignmentReadFilter 2019-11-25T15:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434412-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T15:58:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434432-PairedReadFilter 2019-11-25T15:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434452-AS-ReadPosRankSumTest 2019-11-25T15:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434472-GetPileupSummaries-BETA 2019-11-25T15:58:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434492-VariantFiltration 2019-11-25T15:58:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434512-LikelihoodRankSumTest 2019-11-25T15:55:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434532-BaseRecalibrator 2019-11-25T15:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434552-BQSRPipelineSpark-BETA 2019-11-25T15:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434572-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T15:58:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434592-PossibleDeNovo 2019-11-25T15:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434612-DenoiseReadCounts-BETA 2019-11-25T15:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434632-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T15:59:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434652-IntervalListToBed-Picard 2019-11-25T15:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434672-GermlineCNVCaller-BETA 2019-11-25T15:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434692-MappingQualityZero 2019-11-25T15:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434712-PlatformReadFilter 2019-11-25T15:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434732-BamIndexStats-Picard 2019-11-25T15:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434752-Mutect2 2019-11-25T15:59:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434772-AddOrReplaceReadGroups-Picard 2019-11-25T15:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434792-CollectGcBiasMetrics-Picard 2019-11-25T15:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434812-LiftoverVcf-Picard 2019-11-25T15:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434832-AddOATag-Picard 2019-11-25T15:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434852-Coverage 2019-11-25T15:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434872-ApplyBQSRSpark-BETA 2019-11-25T15:59:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434892-MergeVcfs-Picard 2019-11-25T15:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434912-ValidateVariants 2019-11-25T15:59:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434932-CollectAllelicCounts-BETA 2019-11-25T15:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434952-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T15:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434972-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T15:59:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036434992-QualityScoreDistribution-Picard 2019-11-25T15:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435012-BaitDesigner-Picard 2019-11-25T15:59:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435032-InbreedingCoeff 2019-11-25T15:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435052-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T15:59:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435072-FixMateInformation-Picard 2019-11-25T15:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435092-SortVcf-Picard 2019-11-25T15:59:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435132-FastqToSam-Picard 2019-11-25T15:59:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435152-CollectRnaSeqMetrics-Picard 2019-11-25T15:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435172-AnnotateIntervals-BETA 2019-11-25T15:59:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435192-RevertSam-Picard 2019-11-25T15:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435212-PassesVendorQualityCheckReadFilter 2019-11-25T15:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435232-SplitReads 2019-11-25T15:59:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435252-AS-MappingQualityRankSumTest 2019-11-25T15:59:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435272-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T15:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435292-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T15:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435312-ReadPosRankSumTest 2019-11-25T15:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435332-IntervalOverlapReadFilter 2019-11-25T15:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435352-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T15:59:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435372-PlotDenoisedCopyRatios-BETA 2019-11-25T15:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435392-FastaAlternateReferenceMaker 2019-11-25T15:59:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435412-UnmarkDuplicates 2019-11-25T15:59:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435432-NonZeroFragmentLengthReadFilter 2019-11-25T15:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435452-PileupSpark-BETA 2019-11-25T15:59:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435472-ProperlyPairedReadFilter 2019-11-25T15:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435492-CigarContainsNoNOperator 2019-11-25T15:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435512-SplitVcfs-Picard 2019-11-25T15:59:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435532-FilterFuncotations-EXPERIMENTAL 2019-11-25T15:59:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435552-FindBadGenomicKmersSpark-BETA 2019-11-25T15:59:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435572-AddCommentsToBam-Picard 2019-11-25T15:59:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435592-AnalyzeSaturationMutagenesis-BETA 2019-11-25T15:59:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435612-AS-BaseQualityRankSumTest 2019-11-25T15:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435632-Concordance-BETA 2019-11-25T15:59:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435652-BuildBamIndex-Picard 2019-11-25T15:59:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435672-CollectRrbsMetrics-Picard 2019-11-25T15:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435692-ReferenceBases 2019-11-25T15:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435712-ValidAlignmentEndReadFilter 2019-11-25T15:59:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435732-FastaReferenceMaker 2019-11-25T15:59:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435752-RenameSampleInVcf-Picard 2019-11-25T16:00:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435772-CollectOxoGMetrics-Picard 2019-11-25T15:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435792-CreateReadCountPanelOfNormals-BETA 2019-11-25T15:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435812-ASEReadCounter 2019-11-25T16:00:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036435832-CheckTerminatorBlock-Picard 2019-11-25T15:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447412-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T18:20:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447432-ChromosomeCounts 2019-11-25T18:20:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447452-NonChimericOriginalAlignmentReadFilter 2019-11-25T18:21:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447472-Pileup 2019-11-25T18:25:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447492-BwaMemIndexImageCreator 2019-11-25T18:25:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447512-WellformedReadFilter 2019-11-25T18:25:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447532-AnalyzeCovariates 2019-11-25T18:25:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447552-Funcotator-BETA 2019-11-25T18:25:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447572-CollectQualityYieldMetrics-Picard 2019-11-25T18:21:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447592-SecondOfPairReadFilter 2019-11-25T18:21:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447612-AlignmentAgreesWithHeaderReadFilter 2019-11-25T18:21:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447632-AnnotatePairOrientation-BETA 2019-11-25T18:25:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447652-CountReads 2019-11-25T18:25:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447672-GnarlyGenotyper-BETA 2019-11-25T18:25:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447692-BamToBfq-Picard 2019-11-25T18:21:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447712-VariantAnnotator-BETA 2019-11-25T18:25:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447732-FilterSamReads-Picard 2019-11-25T18:25:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447772-CountBases 2019-11-25T18:25:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447792-UniqueAltReadCount 2019-11-25T18:21:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447812-CountVariantsSpark-BETA 2019-11-25T18:25:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447832-UpdateVCFSequenceDictionary 2019-11-25T18:25:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447852-SamFormatConverter-Picard 2019-11-25T18:21:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447872-ClusterCrosscheckMetrics-Picard 2019-11-25T18:21:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447892-SoftClippedReadFilter 2019-11-25T18:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447912-GetSampleName-BETA 2019-11-25T18:25:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447932-MarkDuplicatesSpark-BETA 2019-11-25T18:25:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447952-DepthPerAlleleBySample 2019-11-25T18:25:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447972-CompareMetrics-Picard 2019-11-25T18:25:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036447992-CalculateFingerprintMetrics-Picard 2019-11-25T18:22:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448012-PathSeqBuildReferenceTaxonomy 2019-11-25T18:22:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448032-AS-FisherStrand 2019-11-25T18:25:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448052-CompareBaseQualities 2019-11-25T18:22:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448072-AnnotateVcfWithBamDepth 2019-11-25T18:25:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448092-CollectSequencingArtifactMetrics-Picard 2019-11-25T18:22:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448112-ExtractSequences-Picard 2019-11-25T18:25:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448132-GatherBQSRReports 2019-11-25T18:22:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448152-CalculateContamination 2019-11-25T18:25:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448172-ApplyBQSR 2019-11-25T18:25:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448192-CpxVariantReInterpreterSpark-BETA 2019-11-25T18:25:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448212-PathSeqBuildKmers 2019-11-25T18:25:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448232-MakeSitesOnlyVcf-Picard 2019-11-25T18:25:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448252-CollectReadCounts-BETA 2019-11-25T18:26:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448272-SortSamSpark-BETA 2019-11-25T18:26:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448292-LeftAlignIndels 2019-11-25T18:26:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448312-MappingQualityNotZeroReadFilter 2019-11-25T18:22:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448332-HaplotypeCallerSpark-BETA 2019-11-25T18:26:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448372-CollectJumpingLibraryMetrics-Picard 2019-11-25T18:22:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448392-SplitSamByNumberOfReads-Picard 2019-11-25T18:26:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448412-MateDifferentStrandReadFilter 2019-11-25T18:26:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448432-NonNFastaSize-Picard 2019-11-25T18:26:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448452-BaseRecalibratorSpark-BETA 2019-11-25T18:26:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448472-CalculateMixingFractions 2019-11-25T18:26:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448512-SelectVariants 2019-11-25T18:26:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448532-AccumulateVariantCallingMetrics-Picard 2019-11-25T18:22:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448552-ReadGroupReadFilter 2019-11-25T18:22:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448572-GenomicsDBImport 2019-11-25T18:26:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448592-CollectQualityYieldMetricsSpark-BETA 2019-11-25T18:26:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448612-PrintReads 2019-11-25T18:26:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448632-CrosscheckReadGroupFingerprints-Picard 2019-11-25T18:22:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448652-ReadsPipelineSpark-BETA 2019-11-25T18:26:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448672-ReplaceSamHeader-Picard 2019-11-25T18:26:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448692-CollectIlluminaLaneMetrics-Picard 2019-11-25T18:26:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448712-CountBasesInReference 2019-11-25T18:26:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448732-PolymorphicNuMT 2019-11-25T18:22:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448752-VcfToIntervalList-Picard 2019-11-25T18:26:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448792-MarkIlluminaAdapters-Picard 2019-11-25T18:26:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448832-FragmentLength 2019-11-25T18:22:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448852-CollectBaseDistributionByCycle-Picard 2019-11-25T18:22:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448872-FixMisencodedBaseQualityReads 2019-11-25T18:26:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448892-LeftAlignAndTrimVariants 2019-11-25T18:26:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448912-ModelSegments-BETA 2019-11-25T18:23:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448932-RevertSamSpark-BETA 2019-11-25T18:26:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448952-RemoveNearbyIndels 2020-05-13T06:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036448972-CollectRawWgsMetrics-Picard 2019-11-25T18:26:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449012-VcfToAdpc-Picard 2019-11-25T18:23:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449032-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:23:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449052-PositionBasedDownsampleSam-Picard 2019-11-25T18:23:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449072-NotSupplementaryAlignmentReadFilter 2019-11-25T18:23:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449092-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T18:26:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449112-PairedReadFilter 2019-11-25T18:23:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449132-GetPileupSummaries-BETA 2019-11-25T18:26:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449152-LikelihoodRankSumTest 2019-11-25T18:23:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449172-RevertBaseQualityScores 2019-11-25T18:26:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449192-GatherTranches-BETA 2019-11-25T18:23:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449212-DownsampleSam-Picard 2019-11-25T18:26:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449232-ClippingRankSumTest 2019-11-25T18:23:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449252-BQSRPipelineSpark-BETA 2019-11-25T18:26:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449272-EstimateLibraryComplexityGATK-BETA 2019-11-25T18:23:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449292-PossibleDeNovo 2019-11-25T18:23:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449312-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T18:26:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449332-IntervalListToBed-Picard 2019-11-25T18:23:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449372-ReadNameReadFilter 2019-11-25T18:23:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449392-CallCopyRatioSegments-BETA 2019-11-25T18:23:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449412-ScatterIntervalsByNs-Picard 2019-11-25T18:26:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449432-AS-InbreedingCoeff 2019-11-25T18:27:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449452-PlatformReadFilter 2019-11-25T18:23:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449472-FilterMutectCalls 2019-11-25T18:27:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449492-CollectVariantCallingMetrics-Picard 2019-11-25T18:23:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449512-CombineGVCFs 2019-11-25T18:27:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449532-CollectGcBiasMetrics-Picard 2019-11-25T18:23:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449552-LiftoverVcf-Picard 2019-11-25T18:27:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449572-AddOATag-Picard 2019-11-25T18:27:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449592-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T18:27:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449612-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T18:23:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449632-CalculateGenotypePosteriors 2019-11-25T18:27:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449652-MergeVcfs-Picard 2019-11-25T18:27:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449672-CollectMultipleMetrics-Picard 2019-11-25T18:27:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449692-ValidateVariants 2019-11-25T18:27:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449712-ExtractSVEvidenceSpark-BETA 2019-11-25T18:27:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449732-CNNScoreVariants-EXPERIMENTAL 2019-11-25T18:27:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449752-QualityScoreDistribution-Picard 2019-11-25T18:24:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449772-FlagStat 2019-11-25T18:27:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449792-BaitDesigner-Picard 2019-11-25T18:27:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449832-FixMateInformation-Picard 2019-11-25T18:24:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449852-PrintVariantsSpark-BETA 2019-11-25T18:27:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449872-FuncotatorDataSourceDownloader-BETA 2019-11-25T18:24:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449892-StrandArtifact 2019-11-25T18:24:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449912-CollectRnaSeqMetrics-Picard 2019-11-25T18:24:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449932-PathSeqScoreSpark 2019-11-25T18:27:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449952-AS-MappingQualityRankSumTest 2019-11-25T18:27:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449972-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T18:27:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036449992-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T18:27:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450012-SeqIsStoredReadFilter 2019-11-25T18:24:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450032-IntervalOverlapReadFilter 2019-11-25T18:24:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450052-VariantRecalibrator 2019-11-25T18:27:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450092-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T18:27:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450112-SplitIntervals 2019-11-25T18:27:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450152-FastaAlternateReferenceMaker 2019-11-25T18:27:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450172-UnmarkDuplicates 2019-11-25T18:27:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450192-EvaluateInfoFieldConcordance-BETA 2019-11-25T18:27:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450212-SplitNCigarReads 2023-12-01T12:47:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450232-NonZeroFragmentLengthReadFilter 2019-11-25T18:24:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450252-PileupSpark-BETA 2019-11-25T18:27:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450272-CigarContainsNoNOperator 2019-11-25T18:24:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450292-FilterFuncotations-EXPERIMENTAL 2019-11-25T18:27:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450312-CrosscheckFingerprints-Picard 2019-11-25T18:27:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450332-FindBadGenomicKmersSpark-BETA 2019-11-25T18:27:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450372-AddCommentsToBam-Picard 2019-11-25T18:27:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450392-AS-QualByDepth 2019-11-25T18:27:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450412-Concordance-BETA 2019-11-25T18:27:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450432-BuildBamIndex-Picard 2019-11-25T18:27:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450452-FindMendelianViolations-Picard 2019-11-25T18:27:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450472-ValidAlignmentEndReadFilter 2019-11-25T18:27:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450492-FastaReferenceMaker 2019-11-25T18:27:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450532-OrientationBiasReadCounts 2019-11-25T18:25:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450552-ASEReadCounter 2019-11-25T18:28:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036450572-CreateSomaticPanelOfNormals-BETA 2019-11-25T18:28:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451152-LibraryReadFilter 2019-11-25T18:32:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451172-NonChimericOriginalAlignmentReadFilter 2019-11-25T18:32:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451192-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T18:36:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451212-OverclippedReadFilter 2019-11-25T18:32:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451232-FirstOfPairReadFilter 2019-11-25T18:32:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451252-Funcotator-BETA 2019-11-25T18:36:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451272-CollectQualityYieldMetrics-Picard 2019-11-25T18:32:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451292-SecondOfPairReadFilter 2019-11-25T18:32:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451312-AlignmentAgreesWithHeaderReadFilter 2019-11-25T18:32:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451332-FilterVcf-Picard 2019-11-25T18:32:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451352-AnnotatePairOrientation-BETA 2019-11-25T18:36:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451372-CollectHsMetrics-Picard 2019-11-25T18:36:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451392-GnarlyGenotyper-BETA 2019-11-25T18:36:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451412-EstimateLibraryComplexity-Picard 2019-11-25T18:36:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451452-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T18:36:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451472-CountVariants 2019-11-25T18:36:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451492-LiftOverIntervalList-Picard 2019-11-25T18:33:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451512-NotDuplicateReadFilter 2019-11-25T18:33:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451532-BamToBfq-Picard 2019-11-25T18:33:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451552-PrimaryLineReadFilter 2019-11-25T18:33:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451572-CollectMultipleMetricsSpark-BETA 2019-11-25T18:36:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451592-StrandOddsRatio 2019-11-25T18:36:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451612-HasReadGroupReadFilter 2019-11-25T18:33:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451632-DetermineGermlineContigPloidy-BETA 2019-11-25T18:33:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451652-FindBreakpointEvidenceSpark-BETA 2019-11-25T18:37:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451672-VariantsToTable 2019-11-25T18:37:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451692-IlluminaBasecallsToFastq-Picard 2019-11-25T18:37:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451712-SamFormatConverter-Picard 2019-11-25T18:33:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451732-FisherStrand 2019-11-25T18:37:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451752-SoftClippedReadFilter 2019-11-25T18:33:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451772-GetSampleName-BETA 2019-11-25T18:37:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451792-MarkDuplicatesSpark-BETA 2019-11-25T18:37:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451812-CalculateReadGroupChecksum-Picard 2019-11-25T18:37:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451832-SetNmMdAndUqTags-Picard 2019-11-25T18:37:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451852-CompareMetrics-Picard 2019-11-25T18:37:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451872-CalculateFingerprintMetrics-Picard 2019-11-25T18:33:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451892-PathSeqBuildReferenceTaxonomy 2019-11-25T18:33:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451912-CompareBaseQualities 2019-11-25T18:33:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451932-BwaSpark-BETA 2019-11-25T18:37:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451952-AnnotateVcfWithBamDepth 2019-11-25T18:37:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451972-GatherVcfs-Picard 2019-11-25T18:33:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036451992-MappedReadFilter 2019-11-25T18:33:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452012-ExtractSequences-Picard 2019-11-25T18:37:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452032-GatherBQSRReports 2019-11-25T18:33:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452072-CalculateContamination 2019-11-25T18:37:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452092-ApplyBQSR 2019-11-25T18:37:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452112-CpxVariantReInterpreterSpark-BETA 2019-11-25T18:37:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452132-PathSeqBuildKmers 2019-11-25T18:37:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452152-IntervalListTools-Picard 2019-11-25T18:37:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452172-CollectReadCounts-BETA 2019-11-25T18:37:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452192-LeftAlignIndels 2019-11-25T18:37:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452212-MappingQualityRankSumTest 2019-11-25T18:37:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452232-MappingQualityNotZeroReadFilter 2019-11-25T18:33:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452252-HaplotypeCallerSpark-BETA 2019-11-25T18:37:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452272-CollectJumpingLibraryMetrics-Picard 2019-11-25T18:33:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452292-IlluminaBasecallsToSam-Picard 2019-11-25T18:37:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452312-GenomicsDBImport 2019-11-25T18:37:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452332-OxoGReadCounts 2019-11-25T18:34:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452352-PrintReads 2019-11-25T18:37:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452372-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T18:37:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452392-HaplotypeCaller 2019-11-25T18:37:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452412-CountFalsePositives-BETA 2019-11-25T18:37:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452432-CountBasesInReference 2019-11-25T18:37:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452452-PolymorphicNuMT 2019-11-25T18:34:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452472-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T18:34:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452492-PathSeqBwaSpark 2019-11-25T18:37:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452532-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T18:37:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452552-FragmentLength 2019-11-25T18:34:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452572-CheckIlluminaDirectory-Picard 2019-11-25T18:37:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452592-LeftAlignAndTrimVariants 2019-11-25T18:37:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452612-RevertSamSpark-BETA 2019-11-25T18:37:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452632-RemoveNearbyIndels 2019-11-25T18:37:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452652-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T18:37:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452672-MarkDuplicates-Picard 2019-11-25T18:38:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452692-CreateSequenceDictionary-Picard 2019-11-25T18:38:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452712-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:34:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452732-PositionBasedDownsampleSam-Picard 2019-11-25T18:34:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452772-PostprocessGermlineCNVCalls-BETA 2019-11-25T18:38:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452792-NotSupplementaryAlignmentReadFilter 2019-11-25T18:34:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452812-FlagStatSpark-BETA 2019-11-25T18:38:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452832-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T18:38:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452852-CollectWgsMetrics-Picard 2019-11-25T18:38:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452872-GetPileupSummaries-BETA 2019-11-25T18:38:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452892-VariantFiltration 2019-11-25T18:38:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452912-RevertBaseQualityScores 2019-11-25T18:38:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452932-CompareSAMs-Picard 2019-11-25T18:38:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452952-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:38:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452972-BaseQualityRankSumTest 2019-11-25T18:34:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036452992-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T18:38:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453012-IntervalListToBed-Picard 2019-11-25T18:35:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453052-ReadNameReadFilter 2019-11-25T18:35:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453072-MappingQualityZero 2019-11-25T18:38:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453092-FilterMutectCalls 2019-11-25T18:38:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453112-Mutect2 2019-11-25T18:38:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453132-VcfFormatConverter-Picard 2019-11-25T18:38:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453152-AddOrReplaceReadGroups-Picard 2019-11-25T18:35:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453172-PlotModeledSegments-BETA 2019-11-25T18:35:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453192-CollectVariantCallingMetrics-Picard 2019-11-25T18:35:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453212-CombineGVCFs 2019-11-25T18:38:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453232-CollectGcBiasMetrics-Picard 2019-11-25T18:35:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453252-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T18:38:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453272-ExtractSVEvidenceSpark-BETA 2019-11-25T18:38:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453312-CNNScoreVariants-EXPERIMENTAL 2019-11-25T18:38:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453332-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T18:35:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453352-FlagStat 2019-11-25T18:38:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453372-InbreedingCoeff 2019-11-25T18:35:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453392-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T18:38:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453412-FixMateInformation-Picard 2019-11-25T18:35:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453432-SortVcf-Picard 2019-11-25T18:38:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453452-PrintVariantsSpark-BETA 2019-11-25T18:38:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453472-FastqToSam-Picard 2019-11-25T18:38:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453492-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T18:35:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453512-StrandArtifact 2019-11-25T18:35:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453532-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T18:35:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453552-CollectRnaSeqMetrics-Picard 2019-11-25T18:35:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453572-GatherVcfsCloud-BETA 2019-11-25T18:38:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453592-RevertSam-Picard 2019-11-25T18:38:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453612-ReadPosRankSumTest 2019-11-25T18:35:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453632-IntervalOverlapReadFilter 2019-11-25T18:35:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453652-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T18:35:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453672-VariantRecalibrator 2019-11-25T18:38:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453692-PathSeqFilterSpark 2019-11-25T18:38:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453712-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T18:38:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453732-PlotDenoisedCopyRatios-BETA 2019-11-25T18:35:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453752-SplitIntervals 2019-11-25T18:38:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453792-FastaAlternateReferenceMaker 2019-11-25T18:38:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453812-EvaluateInfoFieldConcordance-BETA 2019-11-25T18:38:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453832-NonZeroFragmentLengthReadFilter 2019-11-25T18:36:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453892-PileupSpark-BETA 2019-11-25T18:39:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453912-CigarContainsNoNOperator 2019-11-25T18:36:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453932-SplitVcfs-Picard 2019-11-25T18:39:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453952-FilterFuncotations-EXPERIMENTAL 2019-11-25T18:39:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453972-SplitSamByLibrary-Picard 2019-11-25T18:39:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036453992-CrosscheckFingerprints-Picard 2019-11-25T18:39:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454012-TandemRepeat 2019-11-25T18:36:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454052-AnalyzeSaturationMutagenesis-BETA 2019-11-25T18:39:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454072-AS-QualByDepth 2019-11-25T18:39:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454092-AS-BaseQualityRankSumTest 2019-11-25T18:39:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454112-Concordance-BETA 2019-11-25T18:39:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454132-CollectRrbsMetrics-Picard 2019-11-25T18:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454152-FindMendelianViolations-Picard 2019-11-25T18:39:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454172-ReferenceBases 2019-11-25T18:36:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454192-IndexFeatureFile 2019-11-25T18:36:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454212-MetricsReadFilter 2019-11-25T18:36:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454232-ValidAlignmentEndReadFilter 2019-11-25T18:39:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454252-FastaReferenceMaker 2019-11-25T18:39:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454272-QualityScoreDistributionSpark-BETA 2019-11-25T18:39:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454292-DepthPerSampleHC 2019-11-25T18:39:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454312-AlleleFraction 2019-11-25T18:39:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454332-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T18:36:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454352-OrientationBiasReadCounts 2019-11-25T18:36:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454372-RenameSampleInVcf-Picard 2019-11-25T18:39:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454392-MappingQualityAvailableReadFilter 2019-11-25T18:36:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454412-CountReadsSpark-BETA 2019-11-25T18:39:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454432-PrintReadsSpark-BETA 2019-11-25T18:39:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454452-ASEReadCounter 2019-11-25T18:39:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454472-CreateSomaticPanelOfNormals-BETA 2019-11-25T18:39:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454492-CheckPileup 2019-11-25T18:39:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454512-GtcToVcf-Picard 2019-11-25T18:36:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454532-CheckTerminatorBlock-Picard 2019-11-25T18:36:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454812-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T18:40:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454832-LibraryReadFilter 2019-11-25T18:41:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454852-NonChimericOriginalAlignmentReadFilter 2019-11-25T18:41:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454872-MeanQualityByCycle-Picard 2019-11-25T18:45:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454892-AnalyzeCovariates 2019-11-25T18:45:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454912-RMSMappingQuality 2019-11-25T18:45:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454952-Funcotator-BETA 2019-11-25T18:45:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454972-SecondOfPairReadFilter 2019-11-25T18:41:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036454992-AlignmentAgreesWithHeaderReadFilter 2019-11-25T18:41:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455012-VariantEval-BETA 2019-11-25T18:45:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455032-CountReads 2019-11-25T18:45:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455072-EstimateLibraryComplexity-Picard 2019-11-25T18:45:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455092-ViewSam-Picard 2019-11-25T18:45:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455112-AllowAllReadsReadFilter 2019-11-25T18:41:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455132-NotDuplicateReadFilter 2019-11-25T18:41:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455152-BamToBfq-Picard 2019-11-25T18:41:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455172-PrimaryLineReadFilter 2019-11-25T18:41:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455192-CountBases 2019-11-25T18:45:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455212-StrandOddsRatio 2019-11-25T18:45:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455232-CheckFingerprint-Picard 2019-11-25T18:41:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455252-UniqueAltReadCount 2019-11-25T18:41:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455272-QualByDepth 2019-11-25T18:45:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455292-VariantsToTable 2019-11-25T18:45:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455312-NormalizeFasta-Picard 2019-11-25T18:45:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455332-AS-RMSMappingQuality 2019-11-25T18:45:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455352-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T18:45:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455372-CountVariantsSpark-BETA 2019-11-25T18:45:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455392-IlluminaBasecallsToFastq-Picard 2019-11-25T18:45:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455412-CollectSamErrorMetrics-Picard 2019-11-25T18:41:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455432-GetSampleName-BETA 2019-11-25T18:45:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455452-CalculateReadGroupChecksum-Picard 2019-11-25T18:45:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455472-SetNmMdAndUqTags-Picard 2019-11-25T18:45:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455492-CompareMetrics-Picard 2019-11-25T18:45:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455512-CalculateFingerprintMetrics-Picard 2019-11-25T18:41:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455532-PathSeqBuildReferenceTaxonomy 2019-11-25T18:41:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455572-BwaSpark-BETA 2019-11-25T18:45:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455592-CollectSequencingArtifactMetrics-Picard 2019-11-25T18:42:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455612-ExtractSequences-Picard 2019-11-25T18:46:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455632-MarkDuplicatesWithMateCigar-Picard 2019-11-25T18:46:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455652-GatherBQSRReports 2019-11-25T18:42:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455672-CalculateContamination 2019-11-25T18:46:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455692-MakeSitesOnlyVcf-Picard 2019-11-25T18:46:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455712-CollectInsertSizeMetrics-Picard 2019-11-25T18:42:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455732-StrandBiasBySample 2019-11-25T18:46:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455752-CollectReadCounts-BETA 2019-11-25T18:46:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455772-FilterIntervals 2019-11-25T18:42:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455792-MappingQualityRankSumTest 2019-11-25T18:46:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455812-HaplotypeCallerSpark-BETA 2019-11-25T18:46:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455832-SplitSamByNumberOfReads-Picard 2019-11-25T18:46:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455852-CalculateMixingFractions 2019-11-25T18:46:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455872-AccumulateVariantCallingMetrics-Picard 2019-11-25T18:42:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455892-IlluminaBasecallsToSam-Picard 2019-11-25T18:46:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455912-MappingQualityReadFilter 2019-11-25T18:46:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455932-GenomicsDBImport 2019-11-25T18:46:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455952-PlatformUnitReadFilter 2019-11-25T18:42:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036455972-CrosscheckReadGroupFingerprints-Picard 2019-11-25T18:42:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456012-ValidAlignmentStartReadFilter 2019-11-25T18:46:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456052-MateUnmappedAndUnmappedReadFilter 2019-11-25T18:42:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456072-MarkIlluminaAdapters-Picard 2019-11-25T18:46:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456092-SampleList 2019-11-25T18:42:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456112-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T18:46:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456132-MeanQualityByCycleSpark-BETA 2019-11-25T18:46:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456152-FragmentLength 2019-11-25T18:42:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456172-CollectBaseDistributionByCycle-Picard 2019-11-25T18:42:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456212-ModelSegments-BETA 2019-11-25T18:42:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456232-RevertSamSpark-BETA 2019-11-25T18:46:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456252-ExtractIlluminaBarcodes-Picard 2019-11-25T18:46:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456292-AmbiguousBaseReadFilter 2019-11-25T18:43:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456312-BedToIntervalList-Picard 2019-11-25T18:46:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456332-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T18:46:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456352-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T18:46:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456372-CreateSequenceDictionary-Picard 2019-11-25T18:46:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456392-GoodCigarReadFilter 2019-11-25T18:43:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456412-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:43:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456432-PositionBasedDownsampleSam-Picard 2019-11-25T18:43:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456452-ReorderSam-Picard 2019-11-25T18:43:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456472-PostprocessGermlineCNVCalls-BETA 2019-11-25T18:46:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456492-CollectWgsMetrics-Picard 2019-11-25T18:46:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456512-AS-ReadPosRankSumTest 2019-11-25T18:46:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456532-GetPileupSummaries-BETA 2019-11-25T18:46:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456572-ExcessHet 2019-11-25T18:43:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456592-BaseRecalibrator 2019-11-25T18:46:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456612-RevertBaseQualityScores 2019-11-25T18:46:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456632-GatherTranches-BETA 2019-11-25T18:43:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456652-DownsampleSam-Picard 2019-11-25T18:46:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456672-CompareSAMs-Picard 2019-11-25T18:46:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456692-EstimateLibraryComplexityGATK-BETA 2019-11-25T18:43:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456712-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:47:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456732-PossibleDeNovo 2019-11-25T18:43:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456752-CollectInsertSizeMetricsSpark-BETA 2019-11-25T18:47:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456772-DenoiseReadCounts-BETA 2019-11-25T18:43:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456792-BaseQualityRankSumTest 2019-11-25T18:43:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456812-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T18:47:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456832-IntervalListToBed-Picard 2019-11-25T18:43:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456852-ApplyVQSR 2019-11-25T18:47:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456872-GermlineCNVCaller-BETA 2019-11-25T18:43:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456892-ReadNameReadFilter 2019-11-25T18:43:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456912-CallCopyRatioSegments-BETA 2019-11-25T18:43:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456932-PlatformReadFilter 2019-11-25T18:43:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456952-BamIndexStats-Picard 2019-11-25T18:47:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456972-FilterMutectCalls 2019-11-25T18:47:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036456992-VcfFormatConverter-Picard 2019-11-25T18:47:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457012-PlotModeledSegments-BETA 2019-11-25T18:43:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457032-CollectVariantCallingMetrics-Picard 2019-11-25T18:43:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457052-CollectGcBiasMetrics-Picard 2019-11-25T18:43:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457072-AddOATag-Picard 2019-11-25T18:47:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457112-ReadPosition 2019-11-25T18:43:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457132-Coverage 2019-11-25T18:47:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457152-CalculateGenotypePosteriors 2019-11-25T18:47:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457172-MergeVcfs-Picard 2019-11-25T18:47:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457192-CollectMultipleMetrics-Picard 2019-11-25T18:47:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457212-ValidateVariants 2019-11-25T18:47:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457232-CNNScoreVariants-EXPERIMENTAL 2019-11-25T18:47:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457252-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T18:44:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457272-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T18:47:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457292-QualityScoreDistribution-Picard 2019-11-25T18:44:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457312-BaitDesigner-Picard 2019-11-25T18:47:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457332-InbreedingCoeff 2019-11-25T18:44:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457352-SortVcf-Picard 2019-11-25T18:47:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457372-ValidateSamFile-Picard 2019-11-25T18:47:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457392-ReadGroupBlackListReadFilter 2019-11-25T18:44:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457412-SamToFastq-Picard 2019-11-25T18:47:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457432-SortSam-Picard 2019-11-25T18:47:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457452-FuncotatorDataSourceDownloader-BETA 2019-11-25T18:44:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457472-StrandArtifact 2019-11-25T18:44:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457492-RevertSam-Picard 2019-11-25T18:47:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457512-PassesVendorQualityCheckReadFilter 2019-11-25T18:44:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457532-SplitReads 2019-11-25T18:47:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457552-AS-MappingQualityRankSumTest 2019-11-25T18:47:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457572-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T18:47:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457592-BaseQuality 2019-11-25T18:44:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457612-IntervalOverlapReadFilter 2019-11-25T18:44:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457632-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T18:44:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457652-VariantRecalibrator 2019-11-25T18:47:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457672-FastaAlternateReferenceMaker 2019-11-25T18:47:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457692-EvaluateInfoFieldConcordance-BETA 2019-11-25T18:47:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457712-ProperlyPairedReadFilter 2019-11-25T18:44:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457732-FilterFuncotations-EXPERIMENTAL 2019-11-25T18:47:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457752-CrosscheckFingerprints-Picard 2019-11-25T18:47:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457772-AddCommentsToBam-Picard 2019-11-25T18:47:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457792-Concordance-BETA 2019-11-25T18:47:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457812-BuildBamIndex-Picard 2019-11-25T18:47:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457832-NotSecondaryAlignmentReadFilter 2019-11-25T18:44:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457852-ReferenceBases 2019-11-25T18:44:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457872-MetricsReadFilter 2019-11-25T18:44:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457892-ValidAlignmentEndReadFilter 2019-11-25T18:48:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457912-QualityScoreDistributionSpark-BETA 2019-11-25T18:48:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457932-AlleleFraction 2019-11-25T18:48:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457952-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T18:45:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457972-CountNs 2019-11-25T18:45:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036457992-CollectOxoGMetrics-Picard 2019-11-25T18:45:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458012-CreateReadCountPanelOfNormals-BETA 2019-11-25T18:45:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458032-CountReadsSpark-BETA 2019-11-25T18:48:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458052-CreateSomaticPanelOfNormals-BETA 2019-11-25T18:48:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458072-CleanSam-Picard 2019-11-25T18:45:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458272-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T18:50:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458292-ChromosomeCounts 2019-11-25T18:50:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458312-LibraryReadFilter 2019-11-25T18:51:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458332-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T18:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458352-NonChimericOriginalAlignmentReadFilter 2019-11-25T18:51:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458372-MeanQualityByCycle-Picard 2019-11-25T18:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458392-OverclippedReadFilter 2019-11-25T18:51:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458412-SampleReadFilter 2019-11-25T18:51:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458432-RMSMappingQuality 2019-11-25T18:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458452-FirstOfPairReadFilter 2019-11-25T18:51:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458472-CollectQualityYieldMetrics-Picard 2019-11-25T18:51:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458492-CalcMetadataSpark-BETA 2019-11-25T18:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458532-FilterVcf-Picard 2019-11-25T18:51:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458552-FixVcfHeader-Picard 2019-11-25T18:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458572-GnarlyGenotyper-BETA 2019-11-25T18:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458592-EstimateLibraryComplexity-Picard 2019-11-25T18:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458612-ViewSam-Picard 2019-11-25T18:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458632-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T18:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458652-CountVariants 2019-11-25T18:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458672-BamToBfq-Picard 2019-11-25T18:51:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458692-VariantAnnotator-BETA 2019-11-25T18:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458712-FilterSamReads-Picard 2019-11-25T18:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458732-CollectMultipleMetricsSpark-BETA 2019-11-25T18:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458752-CountBases 2019-11-25T18:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458772-FindBreakpointEvidenceSpark-BETA 2019-11-25T18:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458792-UniqueAltReadCount 2019-11-25T18:51:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458812-MappingQuality 2019-11-25T18:51:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458852-VariantsToTable 2019-11-25T18:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458872-NormalizeFasta-Picard 2019-11-25T18:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458892-AS-RMSMappingQuality 2019-11-25T18:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458912-UpdateVCFSequenceDictionary 2019-11-25T18:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458932-FisherStrand 2019-11-25T18:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458952-GetSampleName-BETA 2019-11-25T18:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458972-MarkDuplicatesSpark-BETA 2019-11-25T18:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036458992-GatherBamFiles-Picard 2019-11-25T18:51:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459032-PathSeqBuildReferenceTaxonomy 2019-11-25T18:52:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459052-AS-FisherStrand 2019-11-25T18:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459072-CompareBaseQualities 2019-11-25T18:52:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459092-AnnotateVcfWithBamDepth 2019-11-25T18:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459112-GatherVcfs-Picard 2019-11-25T18:52:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459132-ExtractSequences-Picard 2019-11-25T18:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459152-MarkDuplicatesWithMateCigar-Picard 2019-11-25T18:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459172-ApplyBQSR 2019-11-25T18:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459192-CpxVariantReInterpreterSpark-BETA 2019-11-25T18:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459212-IntervalListTools-Picard 2019-11-25T18:56:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459232-StrandBiasBySample 2019-11-25T18:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459252-LeftAlignIndels 2019-11-25T18:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459272-CollectJumpingLibraryMetrics-Picard 2019-11-25T18:52:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459292-NonNFastaSize-Picard 2019-11-25T18:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459312-BaseRecalibratorSpark-BETA 2019-11-25T18:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459332-CalculateMixingFractions 2019-11-25T18:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459352-AccumulateVariantCallingMetrics-Picard 2019-11-25T18:52:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459372-ReadGroupReadFilter 2019-11-25T18:52:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459392-GenomicsDBImport 2019-11-25T18:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459412-CollectQualityYieldMetricsSpark-BETA 2019-11-25T18:56:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459432-OxoGReadCounts 2019-11-25T18:52:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459452-CreateHadoopBamSplittingIndex-BETA 2019-11-25T18:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459472-PrintReads 2019-11-25T18:56:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459492-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T18:56:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459512-CrosscheckReadGroupFingerprints-Picard 2019-11-25T18:52:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459552-ValidAlignmentStartReadFilter 2019-11-25T18:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459572-ReadsPipelineSpark-BETA 2019-11-25T18:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459592-CountFalsePositives-BETA 2019-11-25T18:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459612-CollectIlluminaLaneMetrics-Picard 2019-11-25T18:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459632-CountBasesInReference 2019-11-25T18:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459652-PolymorphicNuMT 2019-11-25T18:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459672-VcfToIntervalList-Picard 2019-11-25T18:56:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459692-PathSeqBwaSpark 2019-11-25T18:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459712-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T18:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459732-FragmentLength 2019-11-25T18:52:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459752-CollectTargetedPcrMetrics-Picard 2019-11-25T18:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459772-CollectBaseDistributionByCycle-Picard 2019-11-25T18:52:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459792-ReblockGVCF-EXPERIMENTAL 2019-11-25T18:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459812-MergeBamAlignment-Picard 2019-11-25T18:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459832-FixMisencodedBaseQualityReads 2019-11-25T18:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459852-CompareDuplicatesSpark-BETA 2019-11-25T18:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459872-CollectRawWgsMetrics-Picard 2019-11-25T18:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459892-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T18:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459912-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T18:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459932-MarkDuplicates-Picard 2019-11-25T18:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459952-CreateSequenceDictionary-Picard 2019-11-25T18:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459972-VcfToAdpc-Picard 2019-11-25T18:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036459992-PositionBasedDownsampleSam-Picard 2019-11-25T18:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460012-ReorderSam-Picard 2019-11-25T18:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460032-GenotypeSummaries 2019-11-25T18:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460052-FlagStatSpark-BETA 2019-11-25T18:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460072-VariantFiltration 2019-11-25T18:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460092-LikelihoodRankSumTest 2019-11-25T18:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460112-BQSRPipelineSpark-BETA 2019-11-25T18:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460132-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:57:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460152-CollectInsertSizeMetricsSpark-BETA 2019-11-25T18:57:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460172-BaseQualityRankSumTest 2019-11-25T18:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460192-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T18:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460212-IntervalListToBed-Picard 2019-11-25T18:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460232-ApplyVQSR 2019-11-25T18:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460252-MappingQualityZero 2019-11-25T18:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460272-CallCopyRatioSegments-BETA 2019-11-25T18:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460292-FilterMutectCalls 2019-11-25T18:57:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460312-Mutect2 2019-11-25T18:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460332-CombineGVCFs 2019-11-25T18:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460352-CollectGcBiasMetrics-Picard 2019-11-25T18:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460372-ReadPosition 2019-11-25T18:53:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460392-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T18:57:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460412-ReadStrandFilter 2019-11-25T18:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460432-CalculateGenotypePosteriors 2019-11-25T18:57:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460472-ValidateVariants 2019-11-25T18:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460492-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T18:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460512-QualityScoreDistribution-Picard 2019-11-25T18:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460532-BaitDesigner-Picard 2019-11-25T18:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460552-SortVcf-Picard 2019-11-25T18:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460572-SamToFastq-Picard 2019-11-25T18:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460592-SortSam-Picard 2019-11-25T18:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460612-FuncotatorDataSourceDownloader-BETA 2019-11-25T18:54:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460632-StrandArtifact 2019-11-25T18:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460652-MergeSamFiles-Picard 2019-11-25T18:57:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460672-AnnotateIntervals-BETA 2019-11-25T18:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460692-SplitReads 2019-11-25T18:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460752-IntervalOverlapReadFilter 2019-11-25T18:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460772-VariantRecalibrator 2019-11-25T18:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460792-PathSeqFilterSpark 2019-11-25T18:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460812-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T18:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460832-PlotDenoisedCopyRatios-BETA 2019-11-25T18:54:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460852-SplitIntervals 2019-11-25T18:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460872-FastaAlternateReferenceMaker 2019-11-25T18:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460892-UnmarkDuplicates 2019-11-25T18:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460912-EvaluateInfoFieldConcordance-BETA 2019-11-25T18:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460932-NonZeroFragmentLengthReadFilter 2019-11-25T18:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460952-ProperlyPairedReadFilter 2019-11-25T18:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036460972-CigarContainsNoNOperator 2019-11-25T18:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461012-CNNVariantTrain-EXPERIMENTAL 2019-11-25T18:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461032-TandemRepeat 2019-11-25T18:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461052-AddCommentsToBam-Picard 2019-11-25T18:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461072-AnalyzeSaturationMutagenesis-BETA 2019-11-25T18:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461092-AS-QualByDepth 2019-11-25T18:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461112-AS-BaseQualityRankSumTest 2019-11-25T18:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461132-FragmentLengthReadFilter 2019-11-25T18:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461152-NotSecondaryAlignmentReadFilter 2019-11-25T18:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461172-FindMendelianViolations-Picard 2019-11-25T18:58:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461192-IndexFeatureFile 2019-11-25T18:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461212-FastaReferenceMaker 2019-11-25T18:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461232-AlleleFraction 2019-11-25T18:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461252-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T18:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461272-CountNs 2019-11-25T18:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461292-MappingQualityAvailableReadFilter 2019-11-25T18:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461312-CollectOxoGMetrics-Picard 2019-11-25T18:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461332-CountReadsSpark-BETA 2019-11-25T18:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461352-PrintReadsSpark-BETA 2019-11-25T18:58:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461372-GtcToVcf-Picard 2019-11-25T18:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461392-CheckTerminatorBlock-Picard 2019-11-25T18:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461412-ReadLengthReadFilter 2019-11-25T18:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461432-CleanSam-Picard 2019-11-25T18:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461612-CollectIndependentReplicateMetrics-Picard-BETA 2019-11-25T19:01:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461652-LibraryReadFilter 2019-11-25T19:01:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461672-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2019-11-25T19:05:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461692-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T19:05:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461712-OverclippedReadFilter 2019-11-25T19:01:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461732-BwaMemIndexImageCreator 2019-11-25T19:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461752-WellformedReadFilter 2019-11-25T19:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461772-SampleReadFilter 2019-11-25T19:01:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461792-AnalyzeCovariates 2019-11-25T19:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461812-FirstOfPairReadFilter 2019-11-25T19:01:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461832-Funcotator-BETA 2019-11-25T19:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461852-SecondOfPairReadFilter 2019-11-25T19:01:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461872-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T19:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461892-AnnotatePairOrientation-BETA 2019-11-25T19:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461912-VariantEval-BETA 2019-11-25T19:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461932-CountReads 2019-11-25T19:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461952-EstimateLibraryComplexity-Picard 2019-11-25T19:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461972-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T19:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036461992-AllowAllReadsReadFilter 2019-11-25T19:01:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462012-LiftOverIntervalList-Picard 2019-11-25T19:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462032-BamToBfq-Picard 2019-11-25T19:01:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462052-CollectMultipleMetricsSpark-BETA 2019-11-25T19:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462072-CountBases 2019-11-25T19:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462092--Tool-Documentation-Index 2019-12-16T20:19:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462112-FindBreakpointEvidenceSpark-BETA 2019-11-25T19:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462152-MappingQuality 2019-11-25T19:02:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462172-QualByDepth 2019-11-25T19:06:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462192-VariantsToTable 2019-11-25T19:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462212-AS-RMSMappingQuality 2019-11-25T19:06:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462232-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T19:06:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462252-CountVariantsSpark-BETA 2019-11-25T19:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462272-SamFormatConverter-Picard 2019-11-25T19:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462292-FisherStrand 2019-11-25T19:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462312-ClusterCrosscheckMetrics-Picard 2019-11-25T19:02:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462332-GetSampleName-BETA 2019-11-25T19:06:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462352-DepthPerAlleleBySample 2019-11-25T19:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462372-CalculateReadGroupChecksum-Picard 2019-11-25T19:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462392-CompareMetrics-Picard 2019-11-25T19:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462412-CalculateFingerprintMetrics-Picard 2019-11-25T19:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462432-AS-FisherStrand 2019-11-25T19:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462452-CompareBaseQualities 2019-11-25T19:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462472-BwaSpark-BETA 2019-11-25T19:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462492-AnnotateVcfWithBamDepth 2019-11-25T19:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462512-ExtractSequences-Picard 2019-11-25T19:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462532-GatherBQSRReports 2019-11-25T19:02:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462572-CalculateContamination 2019-11-25T19:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462592-IntervalListTools-Picard 2019-11-25T19:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462612-CollectInsertSizeMetrics-Picard 2019-11-25T19:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462632-StrandBiasBySample 2019-11-25T19:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462652-FilterIntervals 2019-11-25T19:02:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462672-MappingQualityNotZeroReadFilter 2019-11-25T19:02:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462692-HaplotypeCallerSpark-BETA 2019-11-25T19:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462712-CollectJumpingLibraryMetrics-Picard 2019-11-25T19:02:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462732-BaseRecalibratorSpark-BETA 2019-11-25T19:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462752-GenomicsDBImport 2019-11-25T19:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462772-ReplaceSamHeader-Picard 2019-11-25T19:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462792-CountFalsePositives-BETA 2019-11-25T19:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462812-MateUnmappedAndUnmappedReadFilter 2019-11-25T19:03:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462832-VcfToIntervalList-Picard 2019-11-25T19:07:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462872-SetNmAndUqTags-Picard 2019-11-25T19:07:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462932-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T19:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462952-MeanQualityByCycleSpark-BETA 2019-11-25T19:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462972-FragmentLength 2019-11-25T19:03:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036462992-CollectTargetedPcrMetrics-Picard 2019-11-25T19:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463012-LeftAlignAndTrimVariants 2019-11-25T19:07:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463032-RemoveNearbyIndels 2019-11-25T19:07:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463052-CollectRawWgsMetrics-Picard 2019-11-25T19:07:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463072-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T19:07:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463092-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2019-11-25T19:03:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463112-PostprocessGermlineCNVCalls-BETA 2019-11-25T19:07:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463132-NotSupplementaryAlignmentReadFilter 2019-11-25T19:03:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463152-FlagStatSpark-BETA 2019-11-25T19:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463172-FifoBuffer-Picard 2019-11-25T19:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463192-BaseRecalibrator 2019-11-25T19:07:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463212-DownsampleSam-Picard 2019-11-25T19:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463232-EstimateLibraryComplexityGATK-BETA 2019-11-25T19:04:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463252-CollectInsertSizeMetricsSpark-BETA 2019-11-25T19:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463272-DenoiseReadCounts-BETA 2019-11-25T19:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463292-IntervalListToBed-Picard 2019-11-25T19:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463312-GermlineCNVCaller-BETA 2019-11-25T19:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463332-UpdateVcfSequenceDictionary-Picard 2019-11-25T19:04:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463352-ReadNameReadFilter 2019-11-25T19:04:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463372-CallCopyRatioSegments-BETA 2019-11-25T19:04:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463392-ScatterIntervalsByNs-Picard 2019-11-25T19:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463412-PlatformReadFilter 2019-11-25T19:04:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463432-Mutect2 2019-11-25T19:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463452-VcfFormatConverter-Picard 2019-11-25T19:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463472-PlotModeledSegments-BETA 2019-11-25T19:04:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463492-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T19:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463512-Coverage 2019-11-25T19:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463532-ReadStrandFilter 2019-11-25T19:04:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463552-ApplyBQSRSpark-BETA 2019-11-25T19:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463572-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T19:04:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463592-CalculateGenotypePosteriors 2019-11-25T19:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463612-MergeVcfs-Picard 2019-11-25T19:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463632-ExtractSVEvidenceSpark-BETA 2019-11-25T19:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463652-CNNScoreVariants-EXPERIMENTAL 2019-11-25T19:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463692-FlagStat 2019-11-25T19:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463712-BaitDesigner-Picard 2019-11-25T19:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463732-FixMateInformation-Picard 2019-11-25T19:04:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463752-SortVcf-Picard 2019-11-25T19:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463772-ValidateSamFile-Picard 2019-11-25T19:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463792-ReadGroupBlackListReadFilter 2019-11-25T19:04:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463832-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T19:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463852-FuncotatorDataSourceDownloader-BETA 2019-11-25T19:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463872-StrandArtifact 2019-11-25T19:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463892-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T19:04:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463912-CollectRnaSeqMetrics-Picard 2019-11-25T19:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463932-RevertSam-Picard 2019-11-25T19:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463952-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T19:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463972-ReadPosRankSumTest 2019-11-25T19:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036463992-IntervalOverlapReadFilter 2019-11-25T19:05:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464012-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T19:05:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464032-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T19:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464052-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T19:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464072-SplitIntervals 2019-11-25T19:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464092-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T19:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464112-EvaluateInfoFieldConcordance-BETA 2019-11-25T19:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464132-SplitNCigarReads 2019-11-25T19:08:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464152-NonZeroFragmentLengthReadFilter 2019-11-25T19:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464172-PileupSpark-BETA 2019-11-25T19:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464192-FilterFuncotations-EXPERIMENTAL 2019-11-25T19:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464232-CNNVariantTrain-EXPERIMENTAL 2019-11-25T19:08:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464252-GenotypeGVCFs 2019-11-25T19:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464272-TandemRepeat 2019-11-25T19:05:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464292-FindBadGenomicKmersSpark-BETA 2019-11-25T19:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464312-AddCommentsToBam-Picard 2019-11-25T19:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464332-AS-QualByDepth 2019-11-25T19:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464352-AS-BaseQualityRankSumTest 2019-11-25T19:08:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464372-Concordance-BETA 2019-11-25T19:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464392-FragmentLengthReadFilter 2019-11-25T19:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464412-CollectRrbsMetrics-Picard 2019-11-25T19:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464432-MetricsReadFilter 2019-11-25T19:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464452-ValidAlignmentEndReadFilter 2019-11-25T19:08:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464472-FastaReferenceMaker 2019-11-25T19:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464492-QualityScoreDistributionSpark-BETA 2019-11-25T19:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464512-DepthPerSampleHC 2019-11-25T19:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464532-OrientationBiasReadCounts 2019-11-25T19:05:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464552-MappingQualityAvailableReadFilter 2019-11-25T19:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464572-CollectOxoGMetrics-Picard 2019-11-25T19:05:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464592-CreateReadCountPanelOfNormals-BETA 2019-11-25T19:05:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464612-FilterVariantTranches-EXPERIMENTAL 2019-11-25T19:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464632-CreateSomaticPanelOfNormals-BETA 2019-11-25T19:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464652-ReadLengthReadFilter 2019-11-25T19:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464672-CleanSam-Picard 2019-11-25T19:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464772-LibraryReadFilter 2019-11-25T19:11:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464792-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2019-11-25T19:16:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464812-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T19:16:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464832-OverclippedReadFilter 2019-11-25T19:12:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464852-BwaMemIndexImageCreator 2019-11-25T19:16:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464872-AnalyzeCovariates 2019-11-25T19:16:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464892-FirstOfPairReadFilter 2019-11-25T19:12:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464912-Funcotator-BETA 2019-11-25T19:16:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464932-CollectQualityYieldMetrics-Picard 2019-11-25T19:12:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464952-PathSeqPipelineSpark 2019-11-25T19:16:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464972-AS-StrandOddsRatio 2019-11-25T19:16:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036464992-AnnotatePairOrientation-BETA 2019-11-25T19:16:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465012-CountReads 2019-11-25T19:16:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465032-GnarlyGenotyper-BETA 2019-11-25T19:16:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465052-ViewSam-Picard 2019-11-25T19:16:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465072-LiftOverIntervalList-Picard 2019-11-25T19:12:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465092-BamToBfq-Picard 2019-11-25T19:12:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465112-VariantAnnotator-BETA 2019-11-25T19:16:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465132-PrimaryLineReadFilter 2019-11-25T19:12:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465152-CollectMultipleMetricsSpark-BETA 2019-11-25T19:16:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465172-DetermineGermlineContigPloidy-BETA 2019-11-25T19:12:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465192-UniqueAltReadCount 2019-11-25T19:12:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465212-MappingQuality 2019-11-25T19:12:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465232-VariantsToTable 2019-11-25T19:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465272-NormalizeFasta-Picard 2019-11-25T19:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465292-AS-RMSMappingQuality 2019-11-25T19:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465312-UpdateVCFSequenceDictionary 2019-11-25T19:16:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465332-IlluminaBasecallsToFastq-Picard 2019-11-25T19:16:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465352-ClusterCrosscheckMetrics-Picard 2019-11-25T19:12:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465372-MarkDuplicatesSpark-BETA 2019-11-25T19:16:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465392-SetNmMdAndUqTags-Picard 2019-11-25T19:16:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465412-FuncotateSegments-BETA 2019-11-25T19:16:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465432-PathSeqBuildReferenceTaxonomy 2019-11-25T19:12:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465452-AS-FisherStrand 2019-11-25T19:16:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465472-CompareBaseQualities 2019-11-25T19:12:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465492-BwaSpark-BETA 2019-11-25T19:16:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465512-CollectAlignmentSummaryMetrics-Picard 2019-11-25T19:12:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465532-CollectSequencingArtifactMetrics-Picard 2019-11-25T19:12:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465552-ExtractSequences-Picard 2019-11-25T19:16:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465572-MarkDuplicatesWithMateCigar-Picard 2019-11-25T19:16:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465592-GatherBQSRReports 2019-11-25T19:13:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465612-CalculateContamination 2019-11-25T19:16:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465632-ApplyBQSR 2019-11-25T19:16:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465652-MakeSitesOnlyVcf-Picard 2019-11-25T19:16:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465672-IntervalListTools-Picard 2019-11-25T19:16:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465692-FilterIntervals 2019-11-25T19:13:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465712-MappingQualityRankSumTest 2019-11-25T19:17:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465732-HaplotypeCallerSpark-BETA 2019-11-25T19:17:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465752-CollectJumpingLibraryMetrics-Picard 2019-11-25T19:13:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465772-FilterMutectCalls 2019-11-25T19:17:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465792-BaseRecalibratorSpark-BETA 2019-11-25T19:17:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465812-CalculateMixingFractions 2019-11-25T19:17:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465832-IlluminaBasecallsToSam-Picard 2019-11-25T19:17:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465852-MappingQualityReadFilter 2019-11-25T19:17:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465872-GenomicsDBImport 2019-11-25T19:17:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465892-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T19:17:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465912-HaplotypeCaller 2019-11-25T19:17:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465932-ReadsPipelineSpark-BETA 2019-11-25T19:17:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465952-ReplaceSamHeader-Picard 2019-11-25T19:17:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465972-CountFalsePositives-BETA 2019-11-25T19:17:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036465992-MateUnmappedAndUnmappedReadFilter 2019-11-25T19:13:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466012-CollectIlluminaLaneMetrics-Picard 2019-11-25T19:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466032-SetNmAndUqTags-Picard 2019-11-25T19:17:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466052-MeanQualityByCycleSpark-BETA 2019-11-25T19:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466072-CheckIlluminaDirectory-Picard 2019-11-25T19:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466092-CollectTargetedPcrMetrics-Picard 2019-11-25T19:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466112-ReblockGVCF-EXPERIMENTAL 2019-11-25T19:17:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466132-MergeBamAlignment-Picard 2019-11-25T19:13:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466152-LeftAlignAndTrimVariants 2019-11-25T19:17:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466172-RevertSamSpark-BETA 2019-11-25T19:17:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466192-AmbiguousBaseReadFilter 2019-11-25T19:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466212-BedToIntervalList-Picard 2019-11-25T19:17:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466232-CompareDuplicatesSpark-BETA 2019-11-25T19:17:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466252-CollectRawWgsMetrics-Picard 2019-11-25T19:17:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466272-MarkDuplicates-Picard 2019-11-25T19:17:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466292-GoodCigarReadFilter 2019-11-25T19:14:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466312-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2019-11-25T19:14:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466332-PositionBasedDownsampleSam-Picard 2019-11-25T19:14:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466352-GenotypeSummaries 2019-11-25T19:14:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466372-FlagStatSpark-BETA 2019-11-25T19:17:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466392-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T19:17:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466412-CollectWgsMetrics-Picard 2019-11-25T19:17:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466432-AS-ReadPosRankSumTest 2019-11-25T19:17:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466452-GetPileupSummaries-BETA 2019-11-25T19:17:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466472-FifoBuffer-Picard 2019-11-25T19:14:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466492-LikelihoodRankSumTest 2019-11-25T19:14:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466512-RevertBaseQualityScores 2019-11-25T19:17:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466532-DownsampleSam-Picard 2019-11-25T19:17:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466552-ClippingRankSumTest 2019-11-25T19:14:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466592-CompareSAMs-Picard 2019-11-25T19:17:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466612-EstimateLibraryComplexityGATK-BETA 2019-11-25T19:14:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466632-CollectInsertSizeMetricsSpark-BETA 2019-11-25T19:17:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466652-DenoiseReadCounts-BETA 2019-11-25T19:14:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466672-BaseQualityRankSumTest 2019-11-25T19:14:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466692-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T19:17:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466712-IntervalListToBed-Picard 2019-11-25T19:14:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466732-GermlineCNVCaller-BETA 2019-11-25T19:14:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466752-ReadNameReadFilter 2019-11-25T19:14:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466772-MappingQualityZero 2019-11-25T19:17:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466792-PlatformReadFilter 2019-11-25T19:14:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466812-FilterMutectCalls 2019-11-25T19:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466832-CollectVariantCallingMetrics-Picard 2019-11-25T19:14:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466852-CombineGVCFs 2019-11-25T19:17:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466872-AddOATag-Picard 2019-11-25T19:17:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466892-Coverage 2019-11-25T19:18:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466912-ReadStrandFilter 2019-11-25T19:14:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466932-ApplyBQSRSpark-BETA 2019-11-25T19:18:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466952-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T19:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466972-CalculateGenotypePosteriors 2019-11-25T19:18:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036466992-MergeVcfs-Picard 2019-11-25T19:18:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467012-ValidateVariants 2019-11-25T19:18:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467032-ExtractSVEvidenceSpark-BETA 2019-11-25T19:18:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467052-CollectAllelicCounts-BETA 2019-11-25T19:18:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467072-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T19:18:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467092-InbreedingCoeff 2019-11-25T19:14:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467132-FixMateInformation-Picard 2019-11-25T19:14:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467152-SortVcf-Picard 2019-11-25T19:18:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467172-ValidateSamFile-Picard 2019-11-25T19:18:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467192-FastqToSam-Picard 2019-11-25T19:18:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467212-ReadGroupBlackListReadFilter 2019-11-25T19:15:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467232-SamToFastq-Picard 2019-11-25T19:18:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467252-SortSam-Picard 2019-11-25T19:18:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467272-StrandArtifact 2019-11-25T19:15:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467292-MergeSamFiles-Picard 2019-11-25T19:18:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467312-CollectRnaSeqMetrics-Picard 2019-11-25T19:15:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467332-RevertSam-Picard 2019-11-25T19:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467352-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T19:18:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467372-SeqIsStoredReadFilter 2019-11-25T19:15:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467392-IntervalOverlapReadFilter 2019-11-25T19:15:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467412-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T19:15:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467432-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T19:18:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467452-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T19:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467472-PlotDenoisedCopyRatios-BETA 2019-11-25T19:15:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467492-SplitIntervals 2019-11-25T19:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467512-EvaluateInfoFieldConcordance-BETA 2019-11-25T19:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467532-SplitNCigarReads 2019-11-25T19:18:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467552-ProperlyPairedReadFilter 2019-11-25T19:15:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467572-CigarContainsNoNOperator 2019-11-25T19:15:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467612-FilterFuncotations-EXPERIMENTAL 2019-11-25T19:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467632-SplitSamByLibrary-Picard 2019-11-25T19:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467652-GenotypeGVCFs 2019-11-25T19:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467672-AS-BaseQualityRankSumTest 2019-11-25T19:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467692-Concordance-BETA 2019-11-25T19:18:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467712-NotSecondaryAlignmentReadFilter 2019-11-25T19:15:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467732-FindMendelianViolations-Picard 2019-11-25T19:18:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467752-IndexFeatureFile 2019-11-25T19:15:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467772-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T19:15:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467792-CountNs 2019-11-25T19:15:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467812-RenameSampleInVcf-Picard 2019-11-25T19:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467852-CollectOxoGMetrics-Picard 2019-11-25T19:15:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467872-PrintReadsSpark-BETA 2019-11-25T19:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467892-ASEReadCounter 2019-11-25T19:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467912-FilterVariantTranches-EXPERIMENTAL 2019-11-25T19:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467932-CreateSomaticPanelOfNormals-BETA 2019-11-25T19:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467952-GtcToVcf-Picard 2019-11-25T19:16:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467972-CheckTerminatorBlock-Picard 2019-11-25T19:16:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036467992-CleanSam-Picard 2019-11-25T19:16:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479512-ChromosomeCounts 2019-11-25T20:04:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479532-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T20:09:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479552-OverclippedReadFilter 2019-11-25T20:05:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479572-BwaMemIndexImageCreator 2019-11-25T20:09:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479592-WellformedReadFilter 2019-11-25T20:09:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479632-FirstOfPairReadFilter 2019-11-25T20:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479672-CollectQualityYieldMetrics-Picard 2019-11-25T20:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479712-CalcMetadataSpark-BETA 2019-11-25T20:09:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479732-SecondOfPairReadFilter 2019-11-25T20:05:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479752-AS-StrandOddsRatio 2019-11-25T20:09:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479772-FilterVcf-Picard 2019-11-25T20:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479792-FixVcfHeader-Picard 2019-11-25T20:09:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479812-CollectHsMetrics-Picard 2019-11-25T20:09:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479832-GnarlyGenotyper-BETA 2019-11-25T20:09:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479852-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T20:09:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479872-AllowAllReadsReadFilter 2019-11-25T20:05:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036479992-BamToBfq-Picard 2019-11-25T20:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480012-VariantAnnotator-BETA 2019-11-25T20:09:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480032-FilterSamReads-Picard 2019-11-25T20:09:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480052-StrandOddsRatio 2019-11-25T20:09:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480072--Tool-Documentation-Index 2019-12-16T20:19:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480092-CheckFingerprint-Picard 2019-11-25T20:05:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480112-DetermineGermlineContigPloidy-BETA 2019-11-25T20:05:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480132-FindBreakpointEvidenceSpark-BETA 2019-11-25T20:09:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480152-UniqueAltReadCount 2019-11-25T20:05:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480172-QualByDepth 2019-11-25T20:09:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480192-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2019-11-25T20:09:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480212-NormalizeFasta-Picard 2019-11-25T20:09:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480232-AS-RMSMappingQuality 2019-11-25T20:09:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480252-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T20:09:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480272-UpdateVCFSequenceDictionary 2019-11-25T20:09:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480292-ClipReads 2019-11-25T20:09:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480312-CollectSamErrorMetrics-Picard 2019-11-25T20:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480332-SoftClippedReadFilter 2019-11-25T20:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480352-GetSampleName-BETA 2019-11-25T20:09:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480392-SetNmMdAndUqTags-Picard 2019-11-25T20:09:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480412-CalculateFingerprintMetrics-Picard 2019-11-25T20:06:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480432-CompareBaseQualities 2019-11-25T20:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480452-GatherVcfs-Picard 2019-11-25T20:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480472-MarkDuplicatesWithMateCigar-Picard 2019-11-25T20:10:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480492-CalculateContamination 2019-11-25T20:10:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480512-CpxVariantReInterpreterSpark-BETA 2019-11-25T20:10:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480532-PathSeqBuildKmers 2019-11-25T20:10:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480552-CollectInsertSizeMetrics-Picard 2019-11-25T20:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480572-FilterMutectCalls 2019-11-25T20:10:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480592-BaseRecalibratorSpark-BETA 2019-11-25T20:10:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480612-SelectVariants 2019-11-25T20:10:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480672-ReadGroupReadFilter 2019-11-25T20:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480692-GenomicsDBImport 2019-11-25T20:10:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480752-CreateHadoopBamSplittingIndex-BETA 2019-11-25T20:10:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480812-CrosscheckReadGroupFingerprints-Picard 2019-11-25T20:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480832-CountFalsePositives-BETA 2019-11-25T20:10:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480852-MateUnmappedAndUnmappedReadFilter 2019-11-25T20:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480872-CollectIlluminaLaneMetrics-Picard 2019-11-25T20:10:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480912-VcfToIntervalList-Picard 2019-11-25T20:10:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480932-SetNmAndUqTags-Picard 2019-11-25T20:10:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480952-PathSeqBwaSpark 2019-11-25T20:10:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480972-MatchingBasesAndQualsReadFilter 2019-11-25T20:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036480992-ReblockGVCF-EXPERIMENTAL 2019-11-25T20:10:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481012-ModelSegments-BETA 2019-11-25T20:07:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481052-RevertSamSpark-BETA 2019-11-25T20:10:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481072-ExtractIlluminaBarcodes-Picard 2019-11-25T20:10:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481092-BedToIntervalList-Picard 2019-11-25T20:10:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481112-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T20:10:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481132-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T20:10:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481152-OriginalAlignment 2019-11-25T20:07:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481172-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T20:07:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481192-NotSupplementaryAlignmentReadFilter 2019-11-25T20:07:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481212-GenotypeSummaries 2019-11-25T20:07:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481232-FlagStatSpark-BETA 2019-11-25T20:10:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481252-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T20:10:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481272-AS-ReadPosRankSumTest 2019-11-25T20:10:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481292-GetPileupSummaries-BETA 2019-11-25T20:10:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481312-FifoBuffer-Picard 2019-11-25T20:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481332-ExcessHet 2019-11-25T20:07:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481352-VariantFiltration 2019-11-25T20:10:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481372-ClippingRankSumTest 2019-11-25T20:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481392-BaseQualityRankSumTest 2019-11-25T20:07:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481412-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T20:11:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481432-IntervalListToBed-Picard 2019-11-25T20:07:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481452-ApplyVQSR 2019-11-25T20:11:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481472-GermlineCNVCaller-BETA 2019-11-25T20:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481492-AS-InbreedingCoeff 2019-11-25T20:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481512-FilterMutectCalls 2019-11-25T20:11:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481532-CollectVariantCallingMetrics-Picard 2019-11-25T20:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481552-CombineGVCFs 2019-11-25T20:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481572-CollectGcBiasMetrics-Picard 2019-11-25T20:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481592-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T20:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481612-CalculateGenotypePosteriors 2019-11-25T20:11:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481632-MergeVcfs-Picard 2019-11-25T20:11:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481652-CollectMultipleMetrics-Picard 2019-11-25T20:11:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481672-ValidateVariants 2019-11-25T20:11:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481692-ExtractSVEvidenceSpark-BETA 2019-11-25T20:11:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481712-CNNScoreVariants-EXPERIMENTAL 2019-11-25T20:11:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481732-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T20:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481752-QualityScoreDistribution-Picard 2019-11-25T20:08:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481772-CombineSegmentBreakpoints-EXPERIMENTAL 2019-11-25T20:11:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481792-BaitDesigner-Picard 2019-11-25T20:11:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481812-InbreedingCoeff 2019-11-25T20:08:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481832-SortVcf-Picard 2019-11-25T20:11:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481852-SamToFastq-Picard 2019-11-25T20:11:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481892-FuncotatorDataSourceDownloader-BETA 2019-11-25T20:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481912-StrandArtifact 2019-11-25T20:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481932-CollectRnaSeqMetrics-Picard 2019-11-25T20:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481952-AnnotateIntervals-BETA 2019-11-25T20:11:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481972-RevertSam-Picard 2019-11-25T20:11:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036481992-SplitReads 2019-11-25T20:11:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482012-AS-MappingQualityRankSumTest 2019-11-25T20:11:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482032-CollectFragmentCounts-BETA 2019-11-25T20:11:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482052-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T20:11:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482072-ReadPosRankSumTest 2019-11-25T20:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482092-BaseQuality 2019-11-25T20:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482112-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T20:08:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482132-VariantRecalibrator 2019-11-25T20:11:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482152-PathSeqFilterSpark 2019-11-25T20:11:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482172-PlotDenoisedCopyRatios-BETA 2019-11-25T20:08:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482192-SplitIntervals 2019-11-25T20:11:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482212-FastaAlternateReferenceMaker 2019-11-25T20:11:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482232-UnmarkDuplicates 2019-11-25T20:11:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482252-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T20:11:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482272-EvaluateInfoFieldConcordance-BETA 2019-11-25T20:11:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482292-NonZeroFragmentLengthReadFilter 2019-11-25T20:08:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482312-CigarContainsNoNOperator 2019-11-25T20:08:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482332-SplitVcfs-Picard 2019-11-25T20:11:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482352-CrosscheckFingerprints-Picard 2019-11-25T20:11:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482372-CNNVariantTrain-EXPERIMENTAL 2019-11-25T20:11:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482392-TandemRepeat 2019-11-25T20:08:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482412-AS-QualByDepth 2019-11-25T20:12:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482432-AS-BaseQualityRankSumTest 2019-11-25T20:12:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482452-BuildBamIndex-Picard 2019-11-25T20:12:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482472-NotSecondaryAlignmentReadFilter 2019-11-25T20:08:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482492-MetricsReadFilter 2019-11-25T20:08:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482532-AlleleFraction 2019-11-25T20:12:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482552-OrientationBiasReadCounts 2019-11-25T20:09:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482572-CountNs 2019-11-25T20:09:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482592-MappingQualityAvailableReadFilter 2019-11-25T20:09:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482612-CollectOxoGMetrics-Picard 2019-11-25T20:09:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482632-PrintReadsSpark-BETA 2019-11-25T20:12:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482652-ASEReadCounter 2019-11-25T20:12:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482672-FilterVariantTranches-EXPERIMENTAL 2019-11-25T20:12:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482692-CreateSomaticPanelOfNormals-BETA 2019-11-25T20:12:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482712-GtcToVcf-Picard 2019-11-25T20:09:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482732-ReadLengthReadFilter 2019-11-25T20:09:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482752-CleanSam-Picard 2019-11-25T20:09:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482932-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T20:16:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482952-NonChimericOriginalAlignmentReadFilter 2019-11-25T20:16:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482972-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T20:20:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036482992-GenotypeConcordance-Picard 2019-11-25T20:20:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483012-Pileup 2019-11-25T20:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483032-BwaMemIndexImageCreator 2019-11-25T20:20:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483052-SampleReadFilter 2019-11-25T20:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483072-AnalyzeCovariates 2019-11-25T20:20:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483092-CollectQualityYieldMetrics-Picard 2019-11-25T20:16:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483112-PathSeqPipelineSpark 2019-11-25T20:20:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483132-AlignmentAgreesWithHeaderReadFilter 2019-11-25T20:16:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483152-AS-StrandOddsRatio 2019-11-25T20:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483172-FilterVcf-Picard 2019-11-25T20:16:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483192-AnnotatePairOrientation-BETA 2019-11-25T20:20:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483212-CountReads 2019-11-25T20:20:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483232-FixVcfHeader-Picard 2019-11-25T20:20:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483252-GnarlyGenotyper-BETA 2019-11-25T20:20:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483272-EstimateLibraryComplexity-Picard 2019-11-25T20:21:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483312-CountVariants 2019-11-25T20:21:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483332-AllowAllReadsReadFilter 2019-11-25T20:16:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483352-LiftOverIntervalList-Picard 2019-11-25T20:16:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483372-NotDuplicateReadFilter 2019-11-25T20:16:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483392-VariantAnnotator-BETA 2019-11-25T20:21:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483412-PrimaryLineReadFilter 2019-11-25T20:16:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483432-CollectMultipleMetricsSpark-BETA 2019-11-25T20:21:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483452-MappingQuality 2019-11-25T20:17:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483472-VariantsToTable 2019-11-25T20:21:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483492-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2019-11-25T20:21:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483512-NormalizeFasta-Picard 2019-11-25T20:21:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483532-AS-RMSMappingQuality 2019-11-25T20:21:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483552-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T20:21:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483572-UpdateVCFSequenceDictionary 2019-11-25T20:21:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483592-FisherStrand 2019-11-25T20:21:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483612-ClipReads 2019-11-25T20:21:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483632-GetSampleName-BETA 2019-11-25T20:21:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483652-DepthPerAlleleBySample 2019-11-25T20:21:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483672-SetNmMdAndUqTags-Picard 2019-11-25T20:21:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483692-FuncotateSegments-BETA 2019-11-25T20:21:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483712-CalculateFingerprintMetrics-Picard 2019-11-25T20:17:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483732-PathSeqBuildReferenceTaxonomy 2019-11-25T20:17:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483752-AS-FisherStrand 2019-11-25T20:21:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483792-CollectAlignmentSummaryMetrics-Picard 2019-11-25T20:17:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483812-AnnotateVcfWithBamDepth 2019-11-25T20:21:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483832-CollectSequencingArtifactMetrics-Picard 2019-11-25T20:17:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483852-GatherVcfs-Picard 2019-11-25T20:17:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483872-MarkDuplicatesWithMateCigar-Picard 2019-11-25T20:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483892-GatherBQSRReports 2019-11-25T20:17:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483912-CalculateContamination 2019-11-25T20:21:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483932-PathSeqBuildKmers 2019-11-25T20:21:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483952-IntervalListTools-Picard 2019-11-25T20:21:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483972-StrandBiasBySample 2019-11-25T20:21:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036483992-SortSamSpark-BETA 2019-11-25T20:21:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484012-LeftAlignIndels 2019-11-25T20:21:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484032-MappingQualityRankSumTest 2019-11-25T20:21:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484052-MappingQualityNotZeroReadFilter 2019-11-25T20:17:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484072-HaplotypeCallerSpark-BETA 2019-11-25T20:21:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484092-CollectJumpingLibraryMetrics-Picard 2019-11-25T20:17:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484112-SplitSamByNumberOfReads-Picard 2019-11-25T20:21:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484132-AccumulateVariantCallingMetrics-Picard 2019-11-25T20:17:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484152-IlluminaBasecallsToSam-Picard 2019-11-25T20:21:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484172-MappingQualityReadFilter 2019-11-25T20:21:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484192-CreateHadoopBamSplittingIndex-BETA 2019-11-25T20:21:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484212-PrintReads 2019-11-25T20:21:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484232-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T20:21:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484252-HaplotypeCaller 2019-11-25T20:21:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484272-ValidAlignmentStartReadFilter 2019-11-25T20:21:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484312-CountFalsePositives-BETA 2019-11-25T20:21:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484332-PolymorphicNuMT 2019-11-25T20:18:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484352-SetNmAndUqTags-Picard 2019-11-25T20:21:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484372-MarkIlluminaAdapters-Picard 2019-11-25T20:21:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484392-SampleList 2019-11-25T20:18:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484412-MatchingBasesAndQualsReadFilter 2019-11-25T20:18:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484432-CheckIlluminaDirectory-Picard 2019-11-25T20:22:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484452-CollectBaseDistributionByCycle-Picard 2019-11-25T20:18:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484472-ReblockGVCF-EXPERIMENTAL 2019-11-25T20:22:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484492-MergeBamAlignment-Picard 2019-11-25T20:18:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484512-FixMisencodedBaseQualityReads 2019-11-25T20:22:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484532-RevertSamSpark-BETA 2019-11-25T20:22:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484572-RemoveNearbyIndels 2019-11-25T20:22:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484592-CompareDuplicatesSpark-BETA 2019-11-25T20:22:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484612-CollectRawWgsMetrics-Picard 2019-11-25T20:22:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484632-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T20:22:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484652-OriginalAlignment 2019-11-25T20:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484672-MarkDuplicates-Picard 2021-08-29T19:04:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484692-CreateSequenceDictionary-Picard 2019-11-25T20:22:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484712-VcfToAdpc-Picard 2019-11-25T20:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484732-PositionBasedDownsampleSam-Picard 2019-11-25T20:18:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484752-ReorderSam-Picard 2019-11-25T20:18:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484772-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T20:22:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484832-AS-ReadPosRankSumTest 2019-11-25T20:22:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484852-GetPileupSummaries-BETA 2019-11-25T20:22:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484872-FifoBuffer-Picard 2019-11-25T20:18:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484892-VariantFiltration 2019-11-25T20:22:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484912-BaseRecalibrator 2019-11-25T20:22:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484932-CompareSAMs-Picard 2019-11-25T20:22:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484952-BQSRPipelineSpark-BETA 2019-11-25T20:22:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484972-EstimateLibraryComplexityGATK-BETA 2019-11-25T20:22:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036484992-CollectInsertSizeMetricsSpark-BETA 2019-11-25T20:22:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485012-DenoiseReadCounts-BETA 2019-11-25T20:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485032-BaseQualityRankSumTest 2019-11-25T20:18:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485052-IntervalListToBed-Picard 2019-11-25T20:18:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485072-ApplyVQSR 2019-11-25T20:22:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485092-UpdateVcfSequenceDictionary-Picard 2019-11-25T20:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485112-ReadNameReadFilter 2019-11-25T20:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485132-MappingQualityZero 2019-11-25T20:22:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485152-Mutect2 2024-12-06T04:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485172-VcfFormatConverter-Picard 2019-11-25T20:22:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485192-AddOATag-Picard 2019-11-25T20:22:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485212-ReadPosition 2019-11-25T20:19:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485232-Coverage 2019-11-25T20:22:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485252-CollectMultipleMetrics-Picard 2019-11-25T20:22:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485272-ValidateVariants 2019-11-25T20:22:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485292-ExtractSVEvidenceSpark-BETA 2019-11-25T20:22:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485312-CNNScoreVariants-EXPERIMENTAL 2019-11-25T20:22:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485332-InbreedingCoeff 2019-11-25T20:19:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485352-ReadGroupBlackListReadFilter 2019-11-25T20:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485372-SamToFastq-Picard 2022-07-24T10:46:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485392-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T20:19:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485412-MergeSamFiles-Picard 2019-11-25T20:23:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485432-CollectRnaSeqMetrics-Picard 2019-11-25T20:19:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485452-GatherVcfsCloud-BETA 2019-11-25T20:23:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485472-PathSeqScoreSpark 2019-11-25T20:23:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485492-PassesVendorQualityCheckReadFilter 2019-11-25T20:19:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485512-SplitReads 2019-11-25T20:23:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485532-AS-MappingQualityRankSumTest 2019-11-25T20:23:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485552-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T20:19:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485572-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T20:23:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485592-PathSeqFilterSpark 2019-11-25T20:23:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485612-FastaAlternateReferenceMaker 2019-11-25T20:23:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485632-UnmarkDuplicates 2019-11-25T20:23:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485652-PileupSpark-BETA 2019-11-25T20:23:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485672-CigarContainsNoNOperator 2019-11-25T20:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485692-SplitVcfs-Picard 2019-11-25T20:23:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485712-SplitSamByLibrary-Picard 2019-11-25T20:23:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485732-CrosscheckFingerprints-Picard 2019-11-25T20:23:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485752-TandemRepeat 2019-11-25T20:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485772-FindBadGenomicKmersSpark-BETA 2019-11-25T20:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485792-AddCommentsToBam-Picard 2019-11-25T20:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485812-AnalyzeSaturationMutagenesis-BETA 2019-11-25T20:23:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485832-AS-QualByDepth 2019-11-25T20:23:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485872-FindMendelianViolations-Picard 2019-11-25T20:23:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485892-IndexFeatureFile 2019-11-25T20:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485912-MetricsReadFilter 2019-11-25T20:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485932-FastaReferenceMaker 2019-11-25T20:23:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485952-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T20:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485972-OrientationBiasReadCounts 2019-11-25T20:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036485992-CountNs 2019-11-25T20:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036486012-CountBasesSpark-BETA 2019-11-25T20:23:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036486032-PrintReadsSpark-BETA 2019-11-25T20:23:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036486052-FilterVariantTranches-EXPERIMENTAL 2019-11-25T20:23:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036486072-CreateSomaticPanelOfNormals-BETA 2019-11-25T20:23:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036486092-CheckPileup 2019-11-25T20:23:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036486112-ReadLengthReadFilter 2019-11-25T20:20:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036486132-CleanSam-Picard 2019-11-25T20:20:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488272-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T21:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488312-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T21:05:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488332-GenotypeConcordance-Picard 2019-11-25T21:05:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488352-RMSMappingQuality 2019-11-25T21:05:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488372-FilterVcf-Picard 2019-11-25T21:01:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488392-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T21:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488412-VariantEval-BETA 2019-11-25T21:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488432-GnarlyGenotyper-BETA 2019-11-25T21:05:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488452-AllowAllReadsReadFilter 2019-11-25T21:01:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488472-LiftOverIntervalList-Picard 2019-11-25T21:01:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488492-NotDuplicateReadFilter 2019-11-25T21:01:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488512-FilterSamReads-Picard 2019-11-25T21:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488532-CollectMultipleMetricsSpark-BETA 2019-11-25T21:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488552-CountBases 2019-11-25T21:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488572-StrandOddsRatio 2019-11-25T21:06:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488612--Tool-Documentation-Index 2019-12-16T20:19:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488652-HasReadGroupReadFilter 2019-11-25T21:01:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488672-DetermineGermlineContigPloidy-BETA 2019-11-25T21:01:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488712-NormalizeFasta-Picard 2019-11-25T21:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488732-AS-RMSMappingQuality 2019-11-25T21:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488752-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T21:06:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488772-UpdateVCFSequenceDictionary 2019-11-25T21:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488792-IlluminaBasecallsToFastq-Picard 2019-11-25T21:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488812-SamFormatConverter-Picard 2019-11-25T21:01:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488832-FisherStrand 2019-11-25T21:06:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488852-GetSampleName-BETA 2019-11-25T21:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488872-MarkDuplicatesSpark-BETA 2019-11-25T21:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488892-CompareMetrics-Picard 2019-11-25T21:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488912-CompareBaseQualities 2019-11-25T21:01:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488932-BwaSpark-BETA 2019-11-25T21:06:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488952-CollectAlignmentSummaryMetrics-Picard 2019-11-25T21:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488972-CollectSequencingArtifactMetrics-Picard 2019-11-25T21:02:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036488992-GatherVcfs-Picard 2019-11-25T21:02:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489012-MappedReadFilter 2019-11-25T21:02:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489032-ExtractSequences-Picard 2019-11-25T21:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489052-MarkDuplicatesWithMateCigar-Picard 2019-11-25T21:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489072-GatherBQSRReports 2019-11-25T21:02:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489092-CalculateContamination 2019-11-25T21:06:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489112-ApplyBQSR 2019-11-25T21:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489132-CpxVariantReInterpreterSpark-BETA 2019-11-25T21:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489172-CollectInsertSizeMetrics-Picard 2019-11-25T21:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489192-CollectReadCounts-BETA 2019-11-25T21:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489212-SortSamSpark-BETA 2019-11-25T21:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489232-LeftAlignIndels 2019-11-25T21:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489252-MappingQualityNotZeroReadFilter 2019-11-25T21:02:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489272-HaplotypeCallerSpark-BETA 2019-11-25T21:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489292-MateDifferentStrandReadFilter 2019-11-25T21:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489312-NonNFastaSize-Picard 2019-11-25T21:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489332-FilterMutectCalls 2019-11-25T21:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489352-BaseRecalibratorSpark-BETA 2019-11-25T21:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489372-SelectVariants 2019-11-25T21:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489392-ReadGroupReadFilter 2019-11-25T21:02:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489412-MappingQualityReadFilter 2019-11-25T21:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489452-CollectQualityYieldMetricsSpark-BETA 2019-11-25T21:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489472-CreateHadoopBamSplittingIndex-BETA 2019-11-25T21:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489492-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T21:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489512-CrosscheckReadGroupFingerprints-Picard 2019-11-25T21:02:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489532-HaplotypeCaller 2019-11-25T21:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489552-ValidAlignmentStartReadFilter 2019-11-25T21:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489572-ReadsPipelineSpark-BETA 2019-11-25T21:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489612-MateUnmappedAndUnmappedReadFilter 2019-11-25T21:02:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489632-PolymorphicNuMT 2019-11-25T21:02:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489652-VcfToIntervalList-Picard 2019-11-25T21:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489672-SetNmAndUqTags-Picard 2019-11-25T21:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489692-SampleList 2019-11-25T21:02:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489712-MatchingBasesAndQualsReadFilter 2019-11-25T21:02:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489732-MeanQualityByCycleSpark-BETA 2019-11-25T21:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489752-FragmentLength 2019-11-25T21:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489772-CollectTargetedPcrMetrics-Picard 2019-11-25T21:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489792-ReblockGVCF-EXPERIMENTAL 2019-11-25T21:07:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489812-ModelSegments-BETA 2019-11-25T21:03:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489832-AmbiguousBaseReadFilter 2019-11-25T21:03:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489852-BedToIntervalList-Picard 2019-11-25T21:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489872-CollectRawWgsMetrics-Picard 2019-11-25T21:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489892-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T21:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489912-OriginalAlignment 2019-11-25T21:03:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489932-VcfToAdpc-Picard 2019-11-25T21:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489952-GoodCigarReadFilter 2019-11-25T21:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489972-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T21:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036489992-PositionBasedDownsampleSam-Picard 2019-11-25T21:03:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490012-PostprocessGermlineCNVCalls-BETA 2019-11-25T21:07:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490032-NotSupplementaryAlignmentReadFilter 2019-11-25T21:03:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490052-FlagStatSpark-BETA 2019-11-25T21:07:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490072-PairedReadFilter 2019-11-25T21:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490092-ExcessHet 2019-11-25T21:03:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490112-LikelihoodRankSumTest 2019-11-25T21:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490132-GatherTranches-BETA 2019-11-25T21:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490152-DownsampleSam-Picard 2019-11-25T21:07:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490172-CompareSAMs-Picard 2019-11-25T21:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490192-BQSRPipelineSpark-BETA 2019-11-25T21:07:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490212-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T21:07:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490232-PossibleDeNovo 2019-11-25T21:03:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490252-CollectInsertSizeMetricsSpark-BETA 2019-11-25T21:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490272-DenoiseReadCounts-BETA 2019-11-25T21:03:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490292-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T21:07:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490312-IntervalListToBed-Picard 2019-11-25T21:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490332-ApplyVQSR 2019-11-25T21:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490352-MappingQualityZero 2019-11-25T21:07:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490372-ScatterIntervalsByNs-Picard 2019-11-25T21:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490392-BamIndexStats-Picard 2019-11-25T21:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490412-FilterMutectCalls 2019-11-25T21:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490432-Mutect2 2019-11-25T21:07:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490452-AddOrReplaceReadGroups-Picard 2019-11-25T21:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490492-AddOATag-Picard 2019-11-25T21:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490512-ReadPosition 2019-11-25T21:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490532-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T21:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490552-ReadStrandFilter 2019-11-25T21:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490572-CalculateGenotypePosteriors 2019-11-25T21:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490592-MergeVcfs-Picard 2019-11-25T21:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490612-CollectMultipleMetrics-Picard 2019-11-25T21:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490632-ExtractSVEvidenceSpark-BETA 2019-11-25T21:07:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490652-CollectAllelicCounts-BETA 2019-11-25T21:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490672-CNNScoreVariants-EXPERIMENTAL 2019-11-25T21:07:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490692-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T21:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490712-PreprocessIntervals-BETA 2019-11-25T21:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490732-CombineSegmentBreakpoints-EXPERIMENTAL 2019-11-25T21:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490752-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T21:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490772-SortVcf-Picard 2019-11-25T21:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490792-FastqToSam-Picard 2019-11-25T21:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490812-ReadGroupBlackListReadFilter 2019-11-25T21:04:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490832-SortSam-Picard 2019-11-25T21:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490852-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T21:04:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490872-MergeSamFiles-Picard 2019-11-25T21:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490892-CollectRnaSeqMetrics-Picard 2019-11-25T21:04:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490912-SplitReads 2019-11-25T21:08:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490952-SeqIsStoredReadFilter 2019-11-25T21:04:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490972-VariantRecalibrator 2019-11-25T21:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036490992-PlotDenoisedCopyRatios-BETA 2019-11-25T21:04:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491012-SplitIntervals 2019-11-25T21:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491032-EvaluateInfoFieldConcordance-BETA 2019-11-25T21:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491052-CigarContainsNoNOperator 2019-11-25T21:04:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491072-FilterFuncotations-EXPERIMENTAL 2019-11-25T21:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491092-TandemRepeat 2019-11-25T21:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491132-FindBadGenomicKmersSpark-BETA 2019-11-25T21:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491232-AS-QualByDepth 2019-11-25T21:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491252-Concordance-BETA 2019-11-25T21:08:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491272-IndexFeatureFile 2019-11-25T21:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491292-FastaReferenceMaker 2019-11-25T21:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491312-AlleleFraction 2019-11-25T21:08:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491332-CollectOxoGMetrics-Picard 2019-11-25T21:05:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491352-CreateReadCountPanelOfNormals-BETA 2019-11-25T21:05:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491372-CountBasesSpark-BETA 2019-11-25T21:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491392-CreateSomaticPanelOfNormals-BETA 2019-11-25T21:08:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491412-CheckPileup 2019-11-25T21:08:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491432-ReadLengthReadFilter 2019-11-25T21:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard 2019-11-25T21:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036507932-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T22:34:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036507952-ChromosomeCounts 2019-11-25T22:34:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036507972-LibraryReadFilter 2019-11-25T22:34:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036507992-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T22:38:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508012-NonChimericOriginalAlignmentReadFilter 2019-11-25T22:34:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508052-Pileup 2019-11-25T22:38:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508072-OverclippedReadFilter 2019-11-25T22:34:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508092-BwaMemIndexImageCreator 2019-11-25T22:38:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508112-WellformedReadFilter 2019-11-25T22:38:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508132-AnalyzeCovariates 2019-11-25T22:38:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508152-FirstOfPairReadFilter 2019-11-25T22:34:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508172-Funcotator-BETA 2019-11-25T22:38:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508192-SecondOfPairReadFilter 2019-11-25T22:34:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508232-AlignmentAgreesWithHeaderReadFilter 2019-11-25T22:34:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508272-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T22:38:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508292-AnnotatePairOrientation-BETA 2019-11-25T22:38:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508312-CollectHsMetrics-Picard 2019-11-25T22:38:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508332-EstimateLibraryComplexity-Picard 2019-11-25T22:38:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508352-ViewSam-Picard 2019-11-25T22:38:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508372-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T22:38:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508392-CountVariants 2019-11-25T22:38:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508412-LiftOverIntervalList-Picard 2019-11-25T22:34:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508432-VariantAnnotator-BETA 2019-11-25T22:38:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508452-CollectMultipleMetricsSpark-BETA 2019-11-25T22:38:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508472-CountBases 2019-11-25T22:38:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508512-UniqueAltReadCount 2019-11-25T22:34:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508532-QualByDepth 2019-11-25T22:38:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508552-AS-RMSMappingQuality 2019-11-25T22:38:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508572-CountVariantsSpark-BETA 2019-11-25T22:38:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508592-ClusterCrosscheckMetrics-Picard 2019-11-25T22:34:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508612-CollectSamErrorMetrics-Picard 2019-11-25T22:34:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508632-SoftClippedReadFilter 2019-11-25T22:34:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508652-MarkDuplicatesSpark-BETA 2019-11-25T22:38:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508672-DepthPerAlleleBySample 2019-11-25T22:38:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508692-SortReadFileSpark-BETA 2019-11-25T22:38:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508712-SetNmMdAndUqTags-Picard 2019-11-25T22:38:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508732-FuncotateSegments-BETA 2019-11-25T22:38:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508752-CalculateFingerprintMetrics-Picard 2019-11-25T22:34:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508772-PathSeqBuildReferenceTaxonomy 2019-11-25T22:34:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508792-AS-FisherStrand 2019-11-25T22:39:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508812-GatherVcfs-Picard 2019-11-25T22:35:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508832-ExtractSequences-Picard 2019-11-25T22:39:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508852-MarkDuplicatesWithMateCigar-Picard 2019-11-25T22:39:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508872-CpxVariantReInterpreterSpark-BETA 2019-11-25T22:39:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508892-PathSeqBuildKmers 2019-11-25T22:39:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508912-IntervalListTools-Picard 2019-11-25T22:39:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508932-CollectInsertSizeMetrics-Picard 2019-11-25T22:35:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508952-CollectReadCounts-BETA 2019-11-25T22:39:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508972-SortSamSpark-BETA 2019-11-25T22:39:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036508992-LeftAlignIndels 2019-11-25T22:39:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509012-MappingQualityRankSumTest 2019-11-25T22:39:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509032-MappingQualityNotZeroReadFilter 2019-11-25T22:35:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509052-HaplotypeCallerSpark-BETA 2019-11-25T22:39:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509072-MateDifferentStrandReadFilter 2019-11-25T22:39:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509092-NonNFastaSize-Picard 2019-11-25T22:39:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509112-FilterMutectCalls 2019-11-25T22:39:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509132-BaseRecalibratorSpark-BETA 2019-11-25T22:39:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509152-IlluminaBasecallsToSam-Picard 2019-11-25T22:39:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509172-CreateHadoopBamSplittingIndex-BETA 2019-11-25T22:39:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509192-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T22:39:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509212-HaplotypeCaller 2019-11-25T22:39:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509232-ReplaceSamHeader-Picard 2019-11-25T22:39:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509252-CountFalsePositives-BETA 2019-11-25T22:39:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509272-MateUnmappedAndUnmappedReadFilter 2019-11-25T22:35:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509292-CountBasesInReference 2019-11-25T22:39:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509312-VcfToIntervalList-Picard 2019-11-25T22:39:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509332-MarkIlluminaAdapters-Picard 2019-11-25T22:39:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509352-MatchingBasesAndQualsReadFilter 2019-11-25T22:35:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509372-CollectBaseDistributionByCycle-Picard 2019-11-25T22:35:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509392-ReblockGVCF-EXPERIMENTAL 2019-11-25T22:39:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509412-LeftAlignAndTrimVariants 2019-11-25T22:39:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509432-ModelSegments-BETA 2019-11-25T22:36:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509452-ExtractIlluminaBarcodes-Picard 2019-11-25T22:39:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509472-AmbiguousBaseReadFilter 2019-11-25T22:36:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509512-RemoveNearbyIndels 2019-11-25T22:39:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509532-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T22:39:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509552-OriginalAlignment 2019-11-25T22:36:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509572-CreateSequenceDictionary-Picard 2019-11-25T22:39:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509592-GoodCigarReadFilter 2019-11-25T22:36:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509612-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T22:36:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509632-PositionBasedDownsampleSam-Picard 2019-11-25T22:36:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509652-ReorderSam-Picard 2019-11-25T22:36:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509672-PostprocessGermlineCNVCalls-BETA 2019-11-25T22:39:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509692-NotSupplementaryAlignmentReadFilter 2019-11-25T22:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509712-FlagStatSpark-BETA 2019-11-25T22:39:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509732-PairedReadFilter 2019-11-25T22:36:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509752-AS-ReadPosRankSumTest 2019-11-25T22:39:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509772-GetPileupSummaries-BETA 2019-11-25T22:39:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509792-ExcessHet 2019-11-25T22:36:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509812-VariantFiltration 2019-11-25T22:39:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509832-LikelihoodRankSumTest 2019-11-25T22:36:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509852-RevertBaseQualityScores 2019-11-25T22:39:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509872-DownsampleSam-Picard 2019-11-25T22:39:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509892-ClippingRankSumTest 2019-11-25T22:36:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509912-CompareSAMs-Picard 2019-11-25T22:39:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509932-EstimateLibraryComplexityGATK-BETA 2019-11-25T22:40:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509972-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T22:40:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036509992-PossibleDeNovo 2019-11-25T22:36:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510012-CollectInsertSizeMetricsSpark-BETA 2019-11-25T22:40:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510032-DenoiseReadCounts-BETA 2019-11-25T22:36:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510052-BaseQualityRankSumTest 2019-11-25T22:36:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510072-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T22:40:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510092-GermlineCNVCaller-BETA 2019-11-25T22:36:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510112-ReadNameReadFilter 2019-11-25T22:36:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510132-Mutect2 2019-11-25T22:40:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510152-VcfFormatConverter-Picard 2019-11-25T22:40:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510232-PlotModeledSegments-BETA 2019-11-25T22:36:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510292-CombineGVCFs 2019-11-25T22:40:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510312-CollectGcBiasMetrics-Picard 2019-11-25T22:36:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510332-AddOATag-Picard 2019-11-25T22:40:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510352-ReadPosition 2019-11-25T22:36:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510372-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T22:40:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510392-ReadStrandFilter 2019-11-25T22:36:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510412-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T22:36:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510452-CalculateGenotypePosteriors 2019-11-25T22:40:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510472-MergeVcfs-Picard 2019-11-25T22:40:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510492-CollectMultipleMetrics-Picard 2019-11-25T22:40:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510512-ValidateVariants 2019-11-25T22:40:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510532-CollectAllelicCounts-BETA 2019-11-25T22:40:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510552-CNNScoreVariants-EXPERIMENTAL 2019-11-25T22:40:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510572-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T22:37:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510592-QualityScoreDistribution-Picard 2019-11-25T22:37:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510612-CombineSegmentBreakpoints-EXPERIMENTAL 2019-11-25T22:40:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510632-InbreedingCoeff 2019-11-25T22:37:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510652-SortVcf-Picard 2019-11-25T22:40:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard 2020-05-09T00:07:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510692-ReadGroupBlackListReadFilter 2019-11-25T22:37:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510712-SamToFastq-Picard 2019-11-25T22:40:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510732-SortSam-Picard 2019-11-25T22:40:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510752-StrandArtifact 2019-11-25T22:37:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510772-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T22:37:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510792-RevertSam-Picard 2019-11-25T22:40:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510812-AS-MappingQualityRankSumTest 2019-11-25T22:40:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510832-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T22:40:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510852-BaseQuality 2019-11-25T22:37:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510872-SeqIsStoredReadFilter 2019-11-25T22:37:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator 2023-12-27T08:36:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510912-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T22:40:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510932-PlotDenoisedCopyRatios-BETA 2019-11-25T22:37:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510952-FastaAlternateReferenceMaker 2019-11-25T22:40:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510972-UnmarkDuplicates 2019-11-25T22:40:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036510992-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T22:40:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511012-EvaluateInfoFieldConcordance-BETA 2019-11-25T22:40:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511032-ProperlyPairedReadFilter 2019-11-25T22:37:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511052-CigarContainsNoNOperator 2019-11-25T22:37:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511072-FilterFuncotations-EXPERIMENTAL 2019-11-25T22:40:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511092-SplitSamByLibrary-Picard 2019-11-25T22:40:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511112-CNNVariantTrain-EXPERIMENTAL 2019-11-25T22:40:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511132-GenotypeGVCFs 2019-11-25T22:40:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511152-TandemRepeat 2019-11-25T22:37:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511172-AddCommentsToBam-Picard 2019-11-25T22:40:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511192-AnalyzeSaturationMutagenesis-BETA 2019-11-25T22:40:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511212-AS-BaseQualityRankSumTest 2019-11-25T22:40:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511232-NotSecondaryAlignmentReadFilter 2019-11-25T22:37:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511252-FindMendelianViolations-Picard 2019-11-25T22:41:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511272-IndexFeatureFile 2019-11-25T22:37:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511292-MetricsReadFilter 2019-11-25T22:37:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511312-QualityScoreDistributionSpark-BETA 2019-11-25T22:41:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511332-CountNs 2019-11-25T22:38:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511352-RenameSampleInVcf-Picard 2019-11-25T22:41:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511372-CollectOxoGMetrics-Picard 2019-11-25T22:38:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511392-CheckPileup 2019-11-25T22:41:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036511412-CheckTerminatorBlock-Picard 2019-11-25T22:38:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036594631-Exception-in-thread-main-java-lang-NoClassDefFoundError-org-xerial-snappy-LoadSnappy 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711051-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-23T21:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711071-ChromosomeCounts 2019-11-23T21:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711091-MeanQualityByCycle-Picard 2019-11-23T21:11:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711111-Pileup 2019-11-23T21:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711131-OverclippedReadFilter 2019-11-23T21:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711151-SampleReadFilter 2019-11-23T21:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711171-AnalyzeCovariates 2019-11-23T21:11:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711191-RMSMappingQuality 2019-11-23T21:11:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711211-CalcMetadataSpark-BETA 2019-11-23T21:11:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711231-FilterVcf-Picard 2019-11-23T21:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711251-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-23T21:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711271-VariantEval-BETA 2019-11-23T21:11:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711291-CountReads 2019-11-23T21:11:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711311-EstimateLibraryComplexity-Picard 2019-11-23T21:11:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711331-ViewSam-Picard 2019-11-23T21:11:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711351-AnnotateVcfWithExpectedAlleleFraction 2019-11-23T21:11:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711371-CountVariants 2019-11-23T21:11:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711391-NotDuplicateReadFilter 2019-11-23T21:07:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711411-BamToBfq-Picard 2019-11-23T21:07:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711431-CollectMultipleMetricsSpark-BETA 2019-11-23T21:11:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711451-FindBreakpointEvidenceSpark-BETA 2019-11-23T21:11:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711471-UniqueAltReadCount 2019-11-23T21:07:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711491-MappingQuality 2019-11-23T21:07:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711511-QualByDepth 2019-11-23T21:11:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711531-VariantsToTable 2020-09-29T18:42:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711551-NormalizeFasta-Picard 2019-11-23T21:11:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711571-AS-RMSMappingQuality 2019-11-23T21:11:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711591-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-23T21:11:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711611-UpdateVCFSequenceDictionary 2019-11-23T21:11:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711631-IlluminaBasecallsToFastq-Picard 2019-11-23T21:11:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711651-SamFormatConverter-Picard 2019-11-23T21:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711671-ClusterCrosscheckMetrics-Picard 2019-11-23T21:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711691-ClipReads 2019-11-23T21:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711711-DepthPerAlleleBySample 2019-11-23T21:11:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711731-AS-FisherStrand 2019-11-23T21:12:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711751-CompareBaseQualities 2019-11-23T21:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711771-BwaSpark-BETA 2019-11-23T21:12:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711791-CollectSequencingArtifactMetrics-Picard 2019-11-23T21:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711811-GatherVcfs-Picard 2019-11-23T21:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711831-MappedReadFilter 2019-11-23T21:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711851-GatherBQSRReports 2019-11-23T21:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711871-IntervalListTools-Picard 2019-11-23T21:12:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711891-CollectReadCounts-BETA 2019-11-23T21:12:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711911-LeftAlignIndels 2019-11-23T21:12:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711931-FilterIntervals-BETA 2019-11-23T21:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711951-MappingQualityNotZeroReadFilter 2019-11-23T21:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711971-HaplotypeCallerSpark-BETA 2019-11-23T21:12:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036711991-NonNFastaSize-Picard 2019-11-23T21:12:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712011-AccumulateVariantCallingMetrics-Picard 2019-11-23T21:08:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712031-ReadGroupReadFilter 2019-11-23T21:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712051-MappingQualityReadFilter 2019-11-23T21:12:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712071-GenomicsDBImport 2019-11-23T21:12:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712091-PlatformUnitReadFilter 2019-11-23T21:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712111-CreateHadoopBamSplittingIndex-BETA 2019-11-23T21:12:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712131-CrosscheckReadGroupFingerprints-Picard 2019-11-23T21:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712151-HaplotypeCaller 2019-11-23T21:12:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712171-CountFalsePositives-BETA 2019-11-23T21:12:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712191-CollectIlluminaLaneMetrics-Picard 2019-11-23T21:12:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712211-CollectIlluminaLaneMetrics-Picard 2019-11-23T21:12:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712231-VcfToIntervalList-Picard 2019-11-23T21:12:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712251-SetNmAndUqTags-Picard 2019-11-23T21:12:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712271-MarkIlluminaAdapters-Picard 2019-11-23T21:12:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712291-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-23T21:12:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712311-MeanQualityByCycleSpark-BETA 2019-11-23T21:12:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712331-CollectTargetedPcrMetrics-Picard 2019-11-23T21:12:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712351-MergeBamAlignment-Picard 2019-11-23T21:08:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712371-LeftAlignAndTrimVariants 2019-11-23T21:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712391-AmbiguousBaseReadFilter 2019-11-23T21:08:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712411-CompareDuplicatesSpark-BETA 2019-11-23T21:12:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712431-CollectRawWgsMetrics-Picard 2019-11-23T21:12:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712451-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-23T21:12:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712471-OriginalAlignment 2019-11-23T21:09:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712491-MarkDuplicates-Picard 2019-11-23T21:12:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard 2021-08-10T05:02:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712551-GoodCigarReadFilter 2019-11-23T21:09:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712571-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T21:09:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712591-NotSupplementaryAlignmentReadFilter 2019-11-23T21:09:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712611-GenotypeSummaries 2019-11-23T21:09:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712631-FlagStatSpark-BETA 2019-11-23T21:12:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712651-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-23T21:12:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712671-PairedReadFilter 2019-11-23T21:09:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712691-AS-ReadPosRankSumTest 2019-11-23T21:12:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712711-GetPileupSummaries-BETA 2019-11-23T21:12:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712731-FifoBuffer-Picard 2019-11-23T21:09:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712751-ExcessHet 2019-11-23T21:09:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712771-VariantFiltration 2019-11-23T21:13:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712791-BaseRecalibrator 2019-11-23T21:13:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712811-GatherTranches-BETA 2019-11-23T21:09:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712831-ClippingRankSumTest 2019-11-23T21:09:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712851-CompareSAMs-Picard 2019-11-23T21:13:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712871-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T21:13:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712891-PossibleDeNovo 2019-11-23T21:09:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712911-CollectInsertSizeMetricsSpark-BETA 2019-11-23T21:13:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712931-BaseQualityRankSumTest 2019-11-23T21:09:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712951-IntervalListToBed-Picard 2019-11-23T21:09:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712971-ApplyVQSR 2019-11-23T21:13:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036712991-GermlineCNVCaller-BETA 2019-11-23T21:09:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713011-ReadNameReadFilter 2019-11-23T21:09:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713031-ScatterIntervalsByNs-Picard 2019-11-23T21:13:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713051-AS-InbreedingCoeff 2019-11-23T21:13:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713071-BamIndexStats-Picard 2019-11-23T21:13:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713091-FilterMutectCalls 2019-11-23T21:13:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713111-Mutect2 2019-11-23T21:13:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713131-Mutect2 2022-12-07T09:31:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713151-VcfFormatConverter-Picard 2019-11-23T21:13:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713171-AddOrReplaceReadGroups-Picard 2019-11-23T21:09:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713191-CollectVariantCallingMetrics-Picard 2019-11-23T21:09:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713211-CombineGVCFs 2019-11-23T21:13:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713231-CollectGcBiasMetrics-Picard 2019-11-23T21:09:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713251-MateOnSameContigOrNoMappedMateReadFilter 2019-11-23T21:13:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713271-ReadStrandFilter 2019-11-23T21:09:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713291-ApplyBQSRSpark-BETA 2019-11-23T21:13:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713311-CalculateGenotypePosteriors 2019-11-23T21:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713331-MergeVcfs-Picard 2021-09-09T21:21:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713351-ExtractSVEvidenceSpark-BETA 2019-11-23T21:13:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713371-CollectAllelicCounts-BETA 2019-11-23T21:13:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713391-CNNScoreVariants-EXPERIMENTAL 2019-11-23T21:13:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713411-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-23T21:09:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713431-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-23T21:13:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713451-FlagStat 2019-11-23T21:13:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard 2019-11-23T21:10:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713491-SortVcf-Picard 2022-06-13T18:39:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713511-ReadGroupBlackListReadFilter 2019-11-23T21:10:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713531-SamToFastq-Picard 2019-11-23T21:13:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713551-SortSam-Picard 2019-11-23T21:13:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713571-MergeSamFiles-Picard 2019-11-23T21:13:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713591-CollectRnaSeqMetrics-Picard 2019-11-23T21:10:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713611-AnnotateIntervals-BETA 2019-11-23T21:13:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713631-RevertSam-Picard 2019-11-23T21:13:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713651-PassesVendorQualityCheckReadFilter 2019-11-23T21:10:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713691-ReadPosRankSumTest 2019-11-23T21:10:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713711-SeqIsStoredReadFilter 2019-11-23T21:10:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713731-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-23T21:13:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713751-PlotDenoisedCopyRatios-BETA 2019-11-23T21:10:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713771-SplitIntervals 2019-11-23T21:13:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713791-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-23T21:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713811-EvaluateInfoFieldConcordance-BETA 2019-11-23T21:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713831-SplitNCigarReads 2019-11-23T21:13:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713851-NonZeroFragmentLengthReadFilter 2019-11-23T21:10:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713871-PileupSpark-BETA 2019-11-23T21:13:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713891-CigarContainsNoNOperator 2019-11-23T21:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713911-FilterFuncotations-EXPERIMENTAL 2019-11-23T21:13:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713931-SplitSamByLibrary-Picard 2019-11-23T21:13:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713951-CrosscheckFingerprints-Picard 2019-11-23T21:13:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713971-CNNVariantTrain-EXPERIMENTAL 2019-11-23T21:14:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036713991-TandemRepeat 2019-11-23T21:10:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714011-FindBadGenomicKmersSpark-BETA 2019-11-23T21:14:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714031-AddCommentsToBam-Picard 2019-11-23T21:14:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714051-AS-BaseQualityRankSumTest 2019-11-23T21:14:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714071-CollectRrbsMetrics-Picard 2019-11-23T21:10:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714091-ReferenceBases 2019-11-23T21:10:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714111-MetricsReadFilter 2019-11-23T21:10:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714131-ValidAlignmentEndReadFilter 2019-11-23T21:14:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714151-ValidAlignmentEndReadFilter 2019-11-23T21:14:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714171-QualityScoreDistributionSpark-BETA 2019-11-23T21:14:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714191-ConvertSequencingArtifactToOxoG-Picard 2019-11-23T21:10:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714211-ConvertSequencingArtifactToOxoG-Picard 2019-11-23T21:11:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714231-CountNs 2019-11-23T21:11:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714251-MappingQualityAvailableReadFilter 2019-11-23T21:11:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714271-CreateReadCountPanelOfNormals-BETA 2019-11-23T21:11:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714291-CountReadsSpark-BETA 2019-11-23T21:14:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714311-CountBasesSpark-BETA 2019-11-23T21:14:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714331-PrintReadsSpark-BETA 2019-11-23T21:14:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714351-ASEReadCounter 2019-11-23T21:14:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714371-CheckPileup 2019-11-23T21:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714391-CheckTerminatorBlock-Picard 2019-11-23T21:11:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714411-ReadLengthReadFilter 2019-11-23T21:11:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714431-CleanSam-Picard 2019-11-23T21:11:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714511-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-23T21:33:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714531-CollectHiSeqXPfFailMetrics-Picard 2019-11-23T21:33:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714551-Pileup 2019-11-23T21:33:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714571-OverclippedReadFilter 2019-11-23T21:29:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714591-WellformedReadFilter 2019-11-23T21:33:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714611-SampleReadFilter 2019-11-23T21:29:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714631-AnalyzeCovariates 2019-11-23T21:33:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714651-RMSMappingQuality 2019-11-23T21:33:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714671-Funcotator 2019-11-23T21:33:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714691-CollectQualityYieldMetrics-Picard 2019-11-23T21:29:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714711-PathSeqPipelineSpark 2019-11-23T21:33:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714731-SecondOfPairReadFilter 2019-11-23T21:29:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714751-AlignmentAgreesWithHeaderReadFilter 2019-11-23T21:29:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714771-AS-StrandOddsRatio 2019-11-23T21:33:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714791-FilterVcf-Picard 2019-11-23T21:29:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714811-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-23T21:33:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714831-AnnotatePairOrientation-EXPERIMENTAL 2019-11-23T21:33:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714851-VariantEval-BETA 2019-11-23T21:33:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714871-CountReads 2019-11-23T21:33:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714891-CollectHsMetrics-Picard 2023-01-17T13:13:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714911-AnnotateVcfWithExpectedAlleleFraction 2019-11-23T21:33:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714931-AllowAllReadsReadFilter 2019-11-23T21:29:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714951-LiftOverIntervalList-Picard 2019-11-23T21:29:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714971-FilterSamReads-Picard 2019-11-23T21:34:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036714991-CollectMultipleMetricsSpark-BETA 2019-11-23T21:34:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715011-CountBases 2019-11-23T21:34:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715031-CheckFingerprint-Picard 2019-11-23T21:29:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715051-FindBreakpointEvidenceSpark-BETA 2019-11-23T21:34:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715071-QualByDepth 2019-11-23T21:34:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715091-AS-RMSMappingQuality 2019-11-23T21:34:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715111-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-23T21:34:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715131-CountVariantsSpark 2019-11-23T21:34:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715151-ClusterCrosscheckMetrics-Picard 2019-11-23T21:30:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715171-CollectSamErrorMetrics-Picard 2019-11-23T21:30:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715211-SoftClippedReadFilter 2019-11-23T21:30:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715231-GetSampleName-BETA 2019-11-23T21:34:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715251-MarkDuplicatesSpark 2019-11-23T21:34:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715271-CalculateReadGroupChecksum-Picard 2019-11-23T21:34:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715291-SetNmMdAndUqTags-Picard 2019-11-23T21:34:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715311-PathSeqBuildReferenceTaxonomy 2019-11-23T21:30:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715331-AS-FisherStrand 2019-11-23T21:34:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715351-CompareBaseQualities 2019-11-23T21:30:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715371-CollectAlignmentSummaryMetrics-Picard 2019-11-23T21:30:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715391-AnnotateVcfWithBamDepth 2019-11-23T21:34:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715411-CollectSequencingArtifactMetrics-Picard 2019-11-23T21:30:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715431-GatherVcfs-Picard 2019-11-23T21:30:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715451-MappedReadFilter 2019-11-23T21:30:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715471-ExtractSequences-Picard 2019-11-23T21:34:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715491-MarkDuplicatesWithMateCigar-Picard 2019-11-23T21:34:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715511-GatherBQSRReports 2019-11-23T21:30:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715531-ApplyBQSR 2019-11-23T21:34:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715551-CpxVariantReInterpreterSpark-BETA 2019-11-23T21:34:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715571-MakeSitesOnlyVcf-Picard 2019-11-23T21:34:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715591-CollectInsertSizeMetrics-Picard 2019-11-23T21:30:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715611-StrandBiasBySample 2019-11-23T21:34:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715631-CollectReadCounts 2019-11-23T21:34:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715651-FilterIntervals 2019-11-23T21:30:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715671-CollectJumpingLibraryMetrics-Picard 2019-11-23T21:30:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715691-SplitSamByNumberOfReads-Picard 2019-11-23T21:34:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715711-MateDifferentStrandReadFilter 2019-11-23T21:34:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715731-FilterMutectCalls 2019-11-23T21:34:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715751-BaseRecalibratorSpark-BETA 2019-11-23T21:34:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715771-AccumulateVariantCallingMetrics-Picard 2019-11-23T21:30:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715791-IlluminaBasecallsToSam-Picard 2019-11-23T21:34:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715811-ReadGroupReadFilter 2019-11-23T21:30:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715831-GenomicsDBImport 2019-11-23T21:34:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715851-PlatformUnitReadFilter 2019-11-23T21:30:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715871-PrintReads 2024-04-10T23:39:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715891-HaplotypeCaller 2019-11-23T21:34:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715911-ValidAlignmentStartReadFilter 2019-11-23T21:34:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715931-ReadsPipelineSpark-BETA 2019-11-23T21:34:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715951-CountFalsePositives-BETA 2019-11-23T21:34:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715971-CountBasesInReference 2019-11-23T21:34:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036715991-MarkIlluminaAdapters-Picard 2019-11-23T21:34:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716011-SampleList 2019-11-23T21:31:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716031-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-23T21:34:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716051-MeanQualityByCycleSpark-BETA 2019-11-23T21:34:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716071-ExtractIlluminaBarcodes-Picard 2019-11-23T21:35:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716091-BedToIntervalList-Picard 2019-11-23T21:35:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716111-CompareDuplicatesSpark-BETA 2019-11-23T21:35:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716131-FilterByOrientationBias-EXPERIMENTAL 2019-11-23T21:35:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716151-OriginalAlignment 2019-11-23T21:31:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716171-GoodCigarReadFilter 2019-11-23T21:31:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716191-PositionBasedDownsampleSam-Picard 2019-11-23T21:31:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716211-NotSupplementaryAlignmentReadFilter 2019-11-23T21:31:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716231-GenotypeSummaries 2019-11-23T21:31:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716251-FlagStatSpark 2019-11-23T21:35:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716271-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-23T21:35:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716291-AS-ReadPosRankSumTest 2019-11-23T21:35:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716311-GetPileupSummaries-BETA 2019-11-23T21:35:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716331-FifoBuffer-Picard 2019-11-23T21:31:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716351-ExcessHet 2019-11-23T21:31:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716371-RevertBaseQualityScores 2019-11-23T21:35:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716391-GatherTranches-BETA 2019-11-23T21:31:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716411-ClippingRankSumTest 2019-11-23T21:31:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716431-CompareSAMs-Picard 2019-11-23T21:35:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716451-PossibleDeNovo 2019-11-23T21:31:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716471-CollectInsertSizeMetricsSpark-BETA 2019-11-23T21:35:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716491-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-23T21:35:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716511-GermlineCNVCaller 2019-11-23T21:31:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716531-UpdateVcfSequenceDictionary-Picard 2019-11-23T21:31:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716551-ReadNameReadFilter 2019-11-23T21:31:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716571-CallCopyRatioSegments 2019-11-23T21:31:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716591-AS-InbreedingCoeff 2019-11-23T21:35:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716611-PlatformReadFilter 2019-11-23T21:31:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716631-VcfFormatConverter-Picard 2019-11-23T21:35:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716651-PlotModeledSegments 2019-11-23T21:32:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716671-CombineGVCFs 2019-11-23T21:35:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716691-AddOATag-Picard 2019-11-23T21:35:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716711-ReadPosition 2019-11-23T21:32:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716731-Coverage 2019-11-23T21:35:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716751-ApplyBQSRSpark-BETA 2019-11-23T21:35:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716771-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-23T21:32:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716791-CollectMultipleMetrics-Picard 2019-11-23T21:35:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716811-ValidateVariants 2019-11-23T21:35:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716831-ExtractSVEvidenceSpark-BETA 2019-11-23T21:35:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716851-CollectAllelicCounts 2019-11-23T21:35:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716871-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-23T21:32:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716891-PrintVariantsSpark 2019-11-23T21:35:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716911-ReadGroupBlackListReadFilter 2019-11-23T21:32:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716931-SamToFastq-Picard 2019-11-23T21:35:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716951-CollectIlluminaBasecallingMetrics-Picard 2019-11-23T21:32:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716971-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-23T21:32:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036716991-CollectRnaSeqMetrics-Picard 2019-11-23T21:32:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717031-AnnotateIntervals 2019-11-23T21:35:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717051-PathSeqScoreSpark 2019-11-23T21:36:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717071-SplitReads 2019-11-23T21:36:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717091-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-23T21:36:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717111-NonZeroReferenceLengthAlignmentReadFilter 2019-11-23T21:32:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717131-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-23T21:36:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717151-PlotDenoisedCopyRatios 2019-11-23T21:32:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717171-FastaAlternateReferenceMaker 2019-11-23T21:36:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717191-UnmarkDuplicates 2019-11-23T21:36:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717211-EvaluateInfoFieldConcordance-BETA 2019-11-23T21:36:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717231-PileupSpark-BETA 2019-11-23T21:36:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717251-SplitVcfs-Picard 2019-11-23T21:36:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717271-CNNVariantTrain-EXPERIMENTAL 2019-11-23T21:36:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717291-TandemRepeat 2019-11-23T21:33:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717311-FindBadGenomicKmersSpark-BETA 2019-11-23T21:36:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717331-AddCommentsToBam-Picard 2019-11-23T21:36:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717351-AnalyzeSaturationMutagenesis-BETA 2019-11-23T21:36:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717371-AS-QualByDepth 2019-11-23T21:36:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717391-AS-BaseQualityRankSumTest 2019-11-23T21:36:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717411-Concordance-BETA 2019-11-23T21:36:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717431-FragmentLengthReadFilter 2019-11-23T21:33:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717451-BuildBamIndex-Picard 2019-11-23T21:36:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717471-CollectRrbsMetrics-Picard 2019-11-23T21:33:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717491-NotSecondaryAlignmentReadFilter 2019-11-23T21:33:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717511-ValidAlignmentEndReadFilter 2019-11-23T21:36:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717531-FastaReferenceMaker 2019-11-23T21:36:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717551-QualityScoreDistributionSpark-BETA 2019-11-23T21:36:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717571-DepthPerSampleHC 2019-11-23T21:36:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717591-ConvertSequencingArtifactToOxoG-Picard 2019-11-23T21:33:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717611-CountNs 2019-11-23T21:33:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717631-CollectOxoGMetrics-Picard 2019-11-23T21:33:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717651-CreateReadCountPanelOfNormals 2019-11-23T21:33:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717671-CountBasesSpark 2019-11-23T21:36:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717691-FilterVariantTranches 2019-11-23T21:36:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717711-CreateSomaticPanelOfNormals-BETA 2019-11-23T21:36:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717731-CheckPileup 2019-11-23T21:36:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717751-GtcToVcf-Picard 2019-11-23T21:33:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036717771-ReadLengthReadFilter 2019-11-23T21:33:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725011-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-23T22:25:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725031-MeanQualityByCycle-Picard 2019-11-23T22:25:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725051-CollectHiSeqXPfFailMetrics-Picard 2019-11-23T22:25:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725071-GenotypeConcordance-Picard 2019-11-23T22:25:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725091-Pileup 2019-11-23T22:25:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725111-OverclippedReadFilter 2019-11-23T22:21:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725131-FirstOfPairReadFilter 2019-11-23T22:21:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725151-Funcotator 2019-11-23T22:26:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725171-CollectQualityYieldMetrics-Picard 2019-11-23T22:21:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725191-PathSeqPipelineSpark 2019-11-23T22:26:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725211-CalcMetadataSpark-BETA 2019-11-23T22:26:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725231-SecondOfPairReadFilter 2019-11-23T22:21:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725251-FilterVcf-Picard 2019-11-23T22:21:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725271-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-23T22:26:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725291-AnnotatePairOrientation-BETA 2019-11-23T22:26:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725311-VariantEval-BETA 2019-11-23T22:26:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725331-CountReads 2019-11-23T22:26:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725351-FixVcfHeader-Picard 2019-11-23T22:26:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725371-CollectHsMetrics-Picard 2019-11-23T22:26:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725391-EstimateLibraryComplexity-Picard 2019-11-23T22:26:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725411-ViewSam-Picard 2019-11-23T22:26:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725431-CountVariants 2019-11-23T22:26:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725451-LiftOverIntervalList-Picard 2019-11-23T22:22:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725471-VariantAnnotator-BETA 2019-11-23T22:26:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725491-FilterSamReads-Picard 2019-11-23T22:26:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725511-CollectMultipleMetricsSpark-BETA 2019-11-23T22:26:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725531--Tool-Documentation-Index 2019-12-16T20:20:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725551-UniqueAltReadCount 2019-11-23T22:22:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725571-QualByDepth 2019-11-23T22:26:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725591-NormalizeFasta-Picard 2019-11-23T22:26:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725611-IlluminaBasecallsToFastq-Picard 2019-11-23T22:26:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725631-FisherStrand 2019-11-23T22:26:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725651-ClusterCrosscheckMetrics-Picard 2019-11-23T22:22:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725671-ClipReads 2019-11-23T22:26:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725691-CollectSamErrorMetrics-Picard 2019-11-23T22:22:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725711-SoftClippedReadFilter 2019-11-23T22:22:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725731-GetSampleName-BETA 2019-11-23T22:26:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725751-DepthPerAlleleBySample 2019-11-23T22:26:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725771-CompareMetrics-Picard 2019-11-23T22:26:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725791-FuncotateSegments-BETA 2019-11-23T22:26:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725811-GatherBamFiles-Picard 2019-11-23T22:22:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725831-CalculateFingerprintMetrics-Picard 2019-11-23T22:22:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725851-GatherVcfs-Picard 2019-11-23T22:22:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725871-MappedReadFilter 2019-11-23T22:22:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725891-ExtractSequences-Picard 2019-11-23T22:26:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725911-ApplyBQSR 2019-11-23T22:26:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725931-PathSeqBuildKmers 2019-11-23T22:26:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725951-FilterIntervals 2019-11-23T22:22:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725971-MappingQualityRankSumTest 2019-11-23T22:26:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036725991-HaplotypeCallerSpark-BETA 2019-11-23T22:26:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726011-SplitSamByNumberOfReads-Picard 2019-11-23T22:26:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726031-MateDifferentStrandReadFilter 2019-11-23T22:26:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726051-NonNFastaSize-Picard 2019-11-23T22:26:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726071-FilterMutectCalls 2019-11-23T22:26:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726091-BaseRecalibratorSpark-BETA 2019-11-23T22:26:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726111-CalculateMixingFractions 2019-11-23T22:26:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726131-SelectVariants 2019-11-23T22:26:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726151-AccumulateVariantCallingMetrics-Picard 2019-11-23T22:23:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726171-ReadGroupReadFilter 2019-11-23T22:23:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726191-MappingQualityReadFilter 2019-11-23T22:27:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726211-PlatformUnitReadFilter 2019-11-23T22:23:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726231-OxoGReadCounts 2019-11-23T22:23:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726251-CrosscheckReadGroupFingerprints-Picard 2019-11-23T22:23:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726271-ValidAlignmentStartReadFilter 2019-11-23T22:27:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726291-ReplaceSamHeader-Picard 2019-11-23T22:27:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726311-CountFalsePositives-BETA 2019-11-23T22:27:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726331-MateUnmappedAndUnmappedReadFilter 2019-11-23T22:23:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726351-CollectIlluminaLaneMetrics-Picard 2019-11-23T22:27:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726371-CountBasesInReference 2019-11-23T22:27:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726391-PolymorphicNuMT 2019-11-23T22:23:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726411-SetNmAndUqTags-Picard 2019-11-23T22:27:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726431-MarkIlluminaAdapters-Picard 2019-11-23T22:27:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726451-SampleList 2019-11-23T22:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726471-MeanQualityByCycleSpark-BETA 2019-11-23T22:27:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726491-CheckIlluminaDirectory-Picard 2019-11-23T22:27:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726511-CollectTargetedPcrMetrics-Picard 2019-11-23T22:27:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726531-CollectBaseDistributionByCycle-Picard 2019-11-23T22:23:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726551-MergeBamAlignment-Picard 2019-11-23T22:23:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726571-LeftAlignAndTrimVariants 2019-11-23T22:27:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726591-RevertSamSpark-BETA 2024-04-10T23:49:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726611-BedToIntervalList-Picard 2019-11-23T22:27:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726631-RemoveNearbyIndels 2019-11-23T22:27:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726651-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-23T22:27:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726671-OriginalAlignment 2019-11-23T22:23:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726691-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T22:23:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726711-PostprocessGermlineCNVCalls 2019-11-23T22:27:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726731-NotSupplementaryAlignmentReadFilter 2019-11-23T22:23:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726751-FlagStatSpark-BETA 2019-11-23T22:27:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726771-CollectWgsMetrics-Picard 2019-11-23T22:27:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726791-PairedReadFilter 2019-11-23T22:23:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726811-AS-ReadPosRankSumTest 2019-11-23T22:27:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726831-FifoBuffer-Picard 2019-11-23T22:23:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726851-ExcessHet 2019-11-23T22:23:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726871-VariantFiltration 2019-11-23T22:27:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726891-BaseRecalibrator 2019-11-23T22:27:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726911-GatherTranches-BETA 2019-11-23T22:24:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726931-BQSRPipelineSpark-BETA 2019-11-23T22:27:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726951-PossibleDeNovo 2019-11-23T22:24:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726971-DenoiseReadCounts 2019-11-23T22:24:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036726991-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-23T22:27:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727011-IntervalListToBed-Picard 2019-11-23T22:24:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727031-GermlineCNVCaller 2019-11-23T22:24:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727051-UpdateVcfSequenceDictionary-Picard 2019-11-23T22:24:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727071-MappingQualityZero 2019-11-23T22:27:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727091-ScatterIntervalsByNs-Picard 2019-11-23T22:27:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727111-PlatformReadFilter 2019-11-23T22:24:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727131-PlotModeledSegments 2019-11-23T22:24:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727151-CollectVariantCallingMetrics-Picard 2019-11-23T22:24:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727171-CombineGVCFs 2019-11-23T22:27:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727191-LiftoverVcf-Picard 2019-11-23T22:27:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727211-AddOATag-Picard 2019-11-23T22:27:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727231-ApplyBQSRSpark-BETA 2019-11-23T22:27:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727251-CalculateGenotypePosteriors 2019-11-23T22:27:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727271-MergeVcfs-Picard 2019-11-23T22:28:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727291-ValidateVariants 2019-11-23T22:28:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727311-ExtractSVEvidenceSpark-BETA 2019-11-23T22:28:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727331-CNNScoreVariants 2019-11-23T22:28:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727351-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-23T22:24:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727371-FixMateInformation-Picard 2019-11-23T22:24:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727391-SortVcf-Picard 2019-11-23T22:28:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727411-ValidateSamFile-Picard 2019-11-23T22:28:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727431-FuncotatorDataSourceDownloader 2019-11-23T22:24:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727451-StrandArtifact 2019-11-23T22:24:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727471-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-23T22:24:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727491-MergeSamFiles-Picard 2019-11-23T22:28:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727511-GatherVcfsCloud-BETA 2019-11-23T22:28:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727531-AnnotateIntervals 2019-11-23T22:28:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727551-PathSeqScoreSpark 2019-11-23T22:28:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727571-RevertSam-Picard 2021-10-03T18:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727591-SplitReads 2019-11-23T22:28:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727611-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-23T22:28:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727631-BaseQuality 2019-11-23T22:25:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727651-SeqIsStoredReadFilter 2019-11-23T22:25:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727671-NonZeroReferenceLengthAlignmentReadFilter 2019-11-23T22:25:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727691-CollectBaseDistributionByCycleSpark-BETA 2019-11-23T22:28:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727711-VariantRecalibrator 2019-11-23T22:28:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727731-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-23T22:28:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727751-SplitIntervals 2019-11-23T22:28:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727771-UnmarkDuplicates 2019-11-23T22:28:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727791-EvaluateInfoFieldConcordance-BETA 2019-11-23T22:28:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727811-SplitNCigarReads 2019-11-23T22:28:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727831-PileupSpark-BETA 2019-11-23T22:28:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727851-ProperlyPairedReadFilter 2019-11-23T22:25:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727871-FilterFuncotations-EXPERIMENTAL 2019-11-23T22:28:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727891-SplitSamByLibrary-Picard 2019-11-23T22:28:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727911-CNNVariantTrain-EXPERIMENTAL 2019-11-23T22:28:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727931-GenotypeGVCFs 2019-11-23T22:28:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727951-TandemRepeat 2019-11-23T22:25:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727971-FindBadGenomicKmersSpark-BETA 2019-11-23T22:28:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036727991-AnalyzeSaturationMutagenesis-BETA 2019-11-23T22:28:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728011-FragmentLengthReadFilter 2019-11-23T22:25:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728031-CollectRrbsMetrics-Picard 2019-11-23T22:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728051-NotSecondaryAlignmentReadFilter 2019-11-23T22:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728071-FindMendelianViolations-Picard 2019-11-23T22:28:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728091-ValidAlignmentEndReadFilter 2019-11-23T22:28:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728111-QualityScoreDistributionSpark-BETA 2019-11-23T22:28:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728131-DepthPerSampleHC 2019-11-23T22:28:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728151-AlleleFraction 2019-11-23T22:28:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728171-OrientationBiasReadCounts 2019-11-23T22:25:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728191-MappingQualityAvailableReadFilter 2019-11-23T22:25:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728211-CreateReadCountPanelOfNormals 2019-11-23T22:25:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728231-CountReadsSpark-BETA 2019-11-23T22:28:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728251-CountBasesSpark-BETA 2019-11-23T22:28:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728271-FilterVariantTranches-EXPERIMENTAL 2019-11-23T22:28:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728291-GtcToVcf-Picard 2019-11-23T22:25:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728311-CheckTerminatorBlock-Picard 2019-11-23T22:25:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728331-ReadLengthReadFilter 2019-11-23T22:25:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728351-CleanSam-Picard 2019-11-23T22:25:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728391-ChromosomeCounts 2019-11-23T22:31:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728411-LibraryReadFilter 2019-11-23T22:31:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728431-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-23T22:35:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728451-NonChimericOriginalAlignmentReadFilter 2019-11-23T22:31:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728471-MeanQualityByCycle-Picard 2019-11-23T22:35:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728491-BwaMemIndexImageCreator 2019-11-23T22:35:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728511-WellformedReadFilter 2019-11-23T22:35:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728531-SampleReadFilter 2019-11-23T22:31:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728551-AnalyzeCovariates 2019-11-23T22:35:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728571-RMSMappingQuality 2019-11-23T22:35:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728591-FirstOfPairReadFilter 2019-11-23T22:31:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728611-PathSeqPipelineSpark 2019-11-23T22:35:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728631-AS-StrandOddsRatio 2019-11-23T22:35:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728651-FilterVcf-Picard 2019-11-23T22:31:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728671-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-23T22:35:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728691-VariantEval-BETA 2019-11-23T22:35:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728711-CountReads 2019-11-23T22:35:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728731-CollectHsMetrics-Picard 2019-11-23T22:35:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728751-ViewSam-Picard 2019-11-23T22:36:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728771-AllowAllReadsReadFilter 2019-11-23T22:31:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728791-LiftOverIntervalList-Picard 2019-11-23T22:31:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728811-FilterSamReads-Picard 2019-11-23T22:36:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728831-PrimaryLineReadFilter 2019-11-23T22:31:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728851-CollectMultipleMetricsSpark-BETA 2019-11-23T22:36:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728871-CountBases 2019-11-23T22:36:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728891--Tool-Documentation-Index 2019-12-16T20:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728911-CheckFingerprint-Picard 2019-11-23T22:32:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728931-HasReadGroupReadFilter 2019-11-23T22:32:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728951-QualByDepth 2019-11-23T22:36:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728971-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-23T22:36:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036728991-SamFormatConverter-Picard 2019-11-23T22:32:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729011-ClusterCrosscheckMetrics-Picard 2019-11-23T22:32:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729031-ClipReads 2019-11-23T22:36:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729051-SoftClippedReadFilter 2019-11-23T22:32:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729071-CalculateReadGroupChecksum-Picard 2019-11-23T22:36:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729091-CompareMetrics-Picard 2019-11-23T22:36:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729111-FuncotateSegments-BETA 2019-11-23T22:36:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729131-AS-FisherStrand 2019-11-23T22:36:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729151-BwaSpark-BETA 2019-11-23T22:36:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729171-AnnotateVcfWithBamDepth 2019-11-23T22:36:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729191-CollectSequencingArtifactMetrics-Picard 2019-11-23T22:32:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729211-GatherVcfs-Picard 2019-11-23T22:32:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729231-CalculateContamination 2019-11-23T22:36:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729251-PathSeqBuildKmers 2019-11-23T22:36:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729271-MakeSitesOnlyVcf-Picard 2019-11-23T22:36:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729291-IntervalListTools-Picard 2019-11-23T22:36:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729311-CollectInsertSizeMetrics-Picard 2019-11-23T22:32:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729331-CollectReadCounts 2019-11-23T22:36:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729351-SortSamSpark-BETA 2019-11-23T22:36:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729371-MappingQualityNotZeroReadFilter 2019-11-23T22:32:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729391-HaplotypeCallerSpark-BETA 2019-11-23T22:36:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729411-BaseRecalibratorSpark-BETA 2019-11-23T22:36:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729431-AccumulateVariantCallingMetrics-Picard 2019-11-23T22:32:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729451-IlluminaBasecallsToSam-Picard 2019-11-23T22:36:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729471-GenomicsDBImport 2019-11-23T22:36:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729491-PlatformUnitReadFilter 2019-11-23T22:32:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729511-CreateHadoopBamSplittingIndex-BETA 2019-11-23T22:36:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729531-PrintReads 2019-11-23T22:36:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729551-ReadsPipelineSpark-BETA 2019-11-23T22:36:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729571-CountFalsePositives-BETA 2019-11-23T22:36:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729591-PolymorphicNuMT 2019-11-23T22:33:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729611-VcfToIntervalList-Picard 2019-11-23T22:36:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729631-PathSeqBwaSpark 2019-11-23T22:36:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729651-MarkIlluminaAdapters-Picard 2019-11-23T22:37:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729671-MatchingBasesAndQualsReadFilter 2019-11-23T22:33:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729691-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-23T22:37:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729711-MeanQualityByCycleSpark-BETA 2019-11-23T22:37:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729731-CollectTargetedPcrMetrics-Picard 2019-11-23T22:37:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729751-ReblockGVCF-EXPERIMENTAL 2019-11-23T22:37:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729771-FixMisencodedBaseQualityReads 2019-11-23T22:37:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729791-LeftAlignAndTrimVariants 2019-11-23T22:37:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729811-ModelSegments 2019-11-23T22:33:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729831-ExtractIlluminaBarcodes-Picard 2019-11-23T22:37:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729851-AmbiguousBaseReadFilter 2019-11-23T22:33:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729871-CollectRawWgsMetrics-Picard 2019-11-23T22:37:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729891-MarkDuplicates-Picard 2019-11-23T22:37:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729911-CreateSequenceDictionary-Picard 2022-11-12T21:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729931-GoodCigarReadFilter 2019-11-23T22:33:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729951-PositionBasedDownsampleSam-Picard 2019-11-23T22:33:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729971-ReorderSam-Picard 2019-11-23T22:33:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036729991-FlagStatSpark-BETA 2019-11-23T22:37:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730011-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-23T22:37:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730031-PairedReadFilter 2019-11-23T22:33:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730051-FifoBuffer-Picard 2019-11-23T22:33:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730071-VariantFiltration 2019-11-23T22:37:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730091-LikelihoodRankSumTest 2019-11-23T22:33:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730111-RevertBaseQualityScores 2019-11-23T22:37:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730131-GatherTranches-BETA 2019-11-23T22:33:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730151-ClippingRankSumTest 2019-11-23T22:33:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730171-BQSRPipelineSpark-BETA 2019-11-23T22:37:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730191-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T22:37:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730211-BaseQualityRankSumTest 2019-11-23T22:33:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730231-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-23T22:37:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730251-IntervalListToBed-Picard 2019-11-23T22:33:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730271-ApplyVQSR 2019-11-23T22:37:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730291-ReadNameReadFilter 2019-11-23T22:34:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730311-CallCopyRatioSegments 2019-11-23T22:34:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730331-ScatterIntervalsByNs-Picard 2019-11-23T22:37:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730351-AS-InbreedingCoeff 2019-11-23T22:37:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730371-BamIndexStats-Picard 2019-11-23T22:37:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730391-FilterMutectCalls 2019-11-23T22:37:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730411-Mutect2 2019-11-23T22:37:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730431-CollectGcBiasMetrics-Picard 2019-11-23T22:34:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730451-ReadPosition 2019-11-23T22:34:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730471-MateOnSameContigOrNoMappedMateReadFilter 2019-11-23T22:37:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730491-Coverage 2019-11-23T22:37:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730511-ReadStrandFilter 2019-11-23T22:34:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730531-CalculateGenotypePosteriors 2019-11-23T22:37:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730551-ValidateVariants 2019-11-23T22:37:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730571-ExtractSVEvidenceSpark-BETA 2019-11-23T22:37:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730591-CNNScoreVariants 2019-11-23T22:37:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730611-MethylationTypeCaller-EXPERIMENTAL 2019-11-23T22:37:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730631-QualityScoreDistribution-Picard 2019-11-23T22:34:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730651-FlagStat 2019-11-23T22:37:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730671-InbreedingCoeff 2019-11-23T22:34:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730691-ReadLengthEqualsCigarLengthReadFilter 2019-11-23T22:37:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730711-FixMateInformation-Picard 2019-11-23T22:34:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730731-SortVcf-Picard 2019-11-23T22:37:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730751-PrintVariantsSpark-BETA 2019-11-23T22:37:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730771-SamToFastq-Picard 2019-11-23T22:38:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730791-SortSam-Picard 2019-11-23T22:38:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730811-CollectIlluminaBasecallingMetrics-Picard 2019-11-23T22:34:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730831-FuncotatorDataSourceDownloader 2019-11-23T22:34:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730851-MergeSamFiles-Picard 2019-11-23T22:38:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730871-GatherVcfsCloud-BETA 2019-11-23T22:38:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730891-AnnotateIntervals 2019-11-23T22:38:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730911-ReadPosRankSumTest 2019-11-23T22:34:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730931-BaseQuality 2019-11-23T22:34:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730951-NonZeroReferenceLengthAlignmentReadFilter 2019-11-23T22:34:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730971-CollectBaseDistributionByCycleSpark-BETA 2019-11-23T22:38:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036730991-VariantRecalibrator 2019-11-23T22:38:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731011-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-23T22:38:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731031-FastaAlternateReferenceMaker 2019-11-23T22:38:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731051-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-23T22:38:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731071-SplitNCigarReads 2019-11-23T22:38:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731091-NonZeroFragmentLengthReadFilter 2019-11-23T22:35:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731111-PileupSpark-BETA 2019-11-23T22:38:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731131-ProperlyPairedReadFilter 2019-11-23T22:35:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731151-CigarContainsNoNOperator 2019-11-23T22:35:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731171-FilterFuncotations-EXPERIMENTAL 2019-11-23T22:38:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731191-SplitSamByLibrary-Picard 2019-11-23T22:38:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731211-GenotypeGVCFs 2019-11-23T22:38:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731231-FindBadGenomicKmersSpark-BETA 2019-11-23T22:38:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731251-AS-QualByDepth 2019-11-23T22:38:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731271-Concordance-BETA 2019-11-23T22:38:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731291-FragmentLengthReadFilter 2019-11-23T22:35:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731311-BuildBamIndex-Picard 2019-11-23T22:38:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731331-CollectRrbsMetrics-Picard 2019-11-23T22:35:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731351-FindMendelianViolations-Picard 2019-11-23T22:38:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731371-ReferenceBases 2019-11-23T22:35:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731391-MetricsReadFilter 2019-11-23T22:35:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731411-ValidAlignmentEndReadFilter 2019-11-23T22:38:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731431-FastaReferenceMaker 2019-11-23T22:38:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731451-QualityScoreDistributionSpark-BETA 2019-11-23T22:38:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731471-OrientationBiasReadCounts 2019-11-23T22:35:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731491-CountNs 2019-11-23T22:35:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731511-RenameSampleInVcf-Picard 2019-11-23T22:38:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731531-CollectOxoGMetrics-Picard 2019-11-23T22:35:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731551-CreateReadCountPanelOfNormals 2019-11-23T22:35:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731571-CountReadsSpark-BETA 2019-11-23T22:38:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731591-ASEReadCounter 2019-11-23T22:38:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731611-CheckPileup 2019-11-23T22:38:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731631-GtcToVcf-Picard 2019-11-23T22:35:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731651-CheckTerminatorBlock-Picard 2019-11-23T22:35:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731671-ReadLengthReadFilter 2019-11-23T22:35:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731691-CleanSam-Picard 2019-11-23T22:35:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731731-NonChimericOriginalAlignmentReadFilter 2019-11-23T22:44:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731751-CollectHiSeqXPfFailMetrics-Picard 2019-11-23T22:48:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731771-GenotypeConcordance-Picard 2019-11-23T22:48:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731791-WellformedReadFilter 2019-11-23T22:48:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731811-SampleReadFilter 2019-11-23T22:44:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731831-AnalyzeCovariates 2019-11-23T22:48:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731851-AlignmentAgreesWithHeaderReadFilter 2019-11-23T22:44:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731871-FilterVcf-Picard 2019-11-23T22:44:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731891-CountReads 2019-11-23T22:48:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731911-CollectHsMetrics-Picard 2019-11-23T22:48:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731931-GnarlyGenotyper-BETA 2019-11-23T22:48:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731951-EstimateLibraryComplexity-Picard 2019-11-23T22:48:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731971-ViewSam-Picard 2019-11-23T22:48:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036731991-AllowAllReadsReadFilter 2019-11-23T22:44:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732011-NotDuplicateReadFilter 2019-11-23T22:44:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732031-PrimaryLineReadFilter 2019-11-23T22:44:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732051-CountBases 2019-11-23T22:48:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732071-StrandOddsRatio 2019-11-23T22:48:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732091-HasReadGroupReadFilter 2019-11-23T22:44:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732111-DetermineGermlineContigPloidy 2019-11-23T22:44:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732131-MappingQuality 2019-11-23T22:44:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732151-VariantsToTable 2019-11-23T22:48:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732171-CountVariantsSpark-BETA 2019-11-23T22:48:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732191-UpdateVCFSequenceDictionary 2019-11-23T22:48:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732211-IlluminaBasecallsToFastq-Picard 2019-11-23T22:48:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732231-FisherStrand 2019-11-23T22:48:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732251-ClusterCrosscheckMetrics-Picard 2019-11-23T22:44:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732271-ClipReads 2019-11-23T22:48:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732291-SoftClippedReadFilter 2019-11-23T22:44:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732311-DepthPerAlleleBySample 2019-11-23T22:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732331-CalculateReadGroupChecksum-Picard 2019-11-23T22:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732351-SetNmMdAndUqTags-Picard 2019-11-23T22:48:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732371-CompareMetrics-Picard 2019-11-23T22:48:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732391-FuncotateSegments-BETA 2019-11-23T22:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732411-GatherBamFiles-Picard 2019-11-23T22:44:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732431-CalculateFingerprintMetrics-Picard 2019-11-23T22:45:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732451-AS-FisherStrand 2019-11-23T22:48:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732471-BwaSpark-BETA 2019-11-23T22:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732491-MappedReadFilter 2019-11-23T22:45:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732511-MarkDuplicatesWithMateCigar-Picard 2019-11-23T22:48:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732531-CalculateContamination 2019-11-23T22:49:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732551-MakeSitesOnlyVcf-Picard 2019-11-23T22:49:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732571-CollectReadCounts 2019-11-23T22:49:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732591-HaplotypeCallerSpark-BETA 2019-11-23T22:49:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732611-SplitSamByNumberOfReads-Picard 2019-11-23T22:49:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732631-NonNFastaSize-Picard 2019-11-23T22:49:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732651-FilterMutectCalls 2019-11-23T22:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732671-BaseRecalibratorSpark-BETA 2019-11-23T22:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732691-CalculateMixingFractions 2019-11-23T22:49:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732711-AccumulateVariantCallingMetrics-Picard 2019-11-23T22:45:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732731-IlluminaBasecallsToSam-Picard 2019-11-23T22:49:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732751-MappingQualityReadFilter 2019-11-23T22:49:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732771-GenomicsDBImport 2020-08-01T09:14:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732791-CollectQualityYieldMetricsSpark-BETA 2019-11-23T22:49:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732811-PlatformUnitReadFilter 2019-11-23T22:45:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732831-OxoGReadCounts 2019-11-23T22:45:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732851-CreateHadoopBamSplittingIndex-BETA 2019-11-23T22:49:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732871-PrintReads 2019-11-23T22:49:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732891-CrosscheckReadGroupFingerprints-Picard 2019-11-23T22:45:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732911-CollectIlluminaLaneMetrics-Picard 2019-11-23T22:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732931-CountBasesInReference 2019-11-23T22:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732951-PolymorphicNuMT 2019-11-23T22:45:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732971-SampleList 2019-11-23T22:45:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036732991-FragmentLength 2019-11-23T22:45:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733011-CheckIlluminaDirectory-Picard 2019-11-23T22:49:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733031-CollectTargetedPcrMetrics-Picard 2019-11-23T22:49:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733051-CollectBaseDistributionByCycle-Picard 2019-11-23T22:45:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733071-MergeBamAlignment-Picard 2019-11-23T22:45:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733091-ModelSegments 2019-11-23T22:45:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733111-RevertSamSpark-BETA 2019-11-23T22:49:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733131-ExtractIlluminaBarcodes-Picard 2019-11-23T22:49:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733151-BedToIntervalList-Picard 2019-11-23T22:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733171-CompareDuplicatesSpark-BETA 2019-11-23T22:49:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733191-CollectRawWgsMetrics-Picard 2019-11-23T22:49:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733211-FilterByOrientationBias-EXPERIMENTAL 2019-11-23T22:49:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733231-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-23T22:49:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733251-GoodCigarReadFilter 2019-11-23T22:46:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733271-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-23T22:46:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733291-GenotypeSummaries 2019-11-23T22:46:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733311-FlagStatSpark-BETA 2019-11-23T22:49:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733331-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-23T22:49:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733351-CollectWgsMetrics-Picard 2019-11-23T22:49:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733371-PairedReadFilter 2019-11-23T22:46:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733391-AS-ReadPosRankSumTest 2019-11-23T22:49:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733411-FifoBuffer-Picard 2019-11-23T22:46:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733431-ExcessHet 2019-11-23T22:46:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733451-VariantFiltration 2019-11-23T22:49:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733471-BaseRecalibrator 2019-11-23T22:49:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733491-RevertBaseQualityScores 2019-11-23T22:49:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733511-GatherTranches-BETA 2019-11-23T22:46:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733531-ClippingRankSumTest 2019-11-23T22:46:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733551-CompareSAMs-Picard 2019-11-23T22:49:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733571-DenoiseReadCounts 2019-11-23T22:46:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733591-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-23T22:50:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733611-UpdateVcfSequenceDictionary-Picard 2019-11-23T22:46:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733631-ReadNameReadFilter 2019-11-23T22:46:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733651-MappingQualityZero 2019-11-23T22:50:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733671-CallCopyRatioSegments 2019-11-23T22:46:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733691-ScatterIntervalsByNs-Picard 2019-11-23T22:50:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733711-AS-InbreedingCoeff 2019-11-23T22:50:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733731-PlatformReadFilter 2019-11-23T22:46:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733751-BamIndexStats-Picard 2019-11-23T22:50:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733771-Mutect2 2019-11-23T22:50:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733791-AddOrReplaceReadGroups-Picard 2019-11-23T22:46:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733811-PlotModeledSegments 2019-11-23T22:46:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733831-CollectGcBiasMetrics-Picard 2019-11-23T22:46:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733851-LiftoverVcf-Picard 2019-11-23T22:50:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733871-MateOnSameContigOrNoMappedMateReadFilter 2019-11-23T22:50:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733891-Coverage 2019-11-23T22:50:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733911-ReadStrandFilter 2019-11-23T22:46:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733931-ApplyBQSRSpark-BETA 2019-11-23T22:50:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733951-CalculateGenotypePosteriors 2019-11-23T22:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733971-ValidateVariants 2019-11-23T22:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036733991-ExtractSVEvidenceSpark-BETA 2019-11-23T22:50:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734011-CNNScoreVariants 2019-11-23T22:50:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734031-PreprocessIntervals 2019-11-23T22:50:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734051-QualityScoreDistribution-Picard 2019-11-23T22:47:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734071-ReadLengthEqualsCigarLengthReadFilter 2019-11-23T22:50:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734091-FixMateInformation-Picard 2019-11-23T22:47:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734111-SortVcf-Picard 2019-11-23T22:50:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734131-FastqToSam-Picard 2019-11-23T22:50:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734151-SamToFastq-Picard 2019-11-23T22:50:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734171-FuncotatorDataSourceDownloader 2019-11-23T22:47:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734191-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-23T22:47:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734211-MergeSamFiles-Picard 2019-11-23T22:50:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734231-CollectRnaSeqMetrics-Picard 2019-11-23T22:47:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734251-AnnotateIntervals 2019-11-23T22:50:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734271-PathSeqScoreSpark 2019-11-23T22:50:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734291-RevertSam-Picard 2019-11-23T22:50:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734311-SplitReads 2019-11-23T22:50:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734331-AS-MappingQualityRankSumTest 2019-11-23T22:50:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734351-BaseQuality 2019-11-23T22:47:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734371-IntervalOverlapReadFilter 2019-11-23T22:47:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734391-NonZeroReferenceLengthAlignmentReadFilter 2019-11-23T22:47:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734411-VariantRecalibrator 2019-11-23T22:50:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734431-PathSeqFilterSpark 2019-11-23T22:50:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734451-EvaluateInfoFieldConcordance-BETA 2019-11-23T22:50:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734471-SplitNCigarReads 2019-11-23T22:50:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734491-PileupSpark-BETA 2019-11-23T22:50:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734511-ProperlyPairedReadFilter 2019-11-23T22:47:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734531-CigarContainsNoNOperator 2019-11-23T22:47:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734551-SplitVcfs-Picard 2019-11-23T22:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734571-SplitSamByLibrary-Picard 2019-11-23T22:50:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734591-CrosscheckFingerprints-Picard 2019-11-23T22:50:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734611-CNNVariantTrain-EXPERIMENTAL 2019-11-23T22:50:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734631-GenotypeGVCFs 2019-11-23T22:50:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734651-AddCommentsToBam-Picard 2019-11-23T22:50:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734671-Concordance-BETA 2019-11-23T22:51:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734691-BuildBamIndex-Picard 2019-11-23T22:51:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734711-CollectRrbsMetrics-Picard 2019-11-23T22:47:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734731-NotSecondaryAlignmentReadFilter 2019-11-23T22:47:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734751-ReferenceBases 2019-11-23T22:47:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734771-ValidAlignmentEndReadFilter 2019-11-23T22:51:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734791-CountNs 2019-11-23T22:48:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734811-CollectOxoGMetrics-Picard 2019-11-23T22:48:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734831-CountReadsSpark-BETA 2019-11-23T22:51:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734851-ASEReadCounter 2019-11-23T22:51:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734871-CheckPileup 2019-11-23T22:51:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734891-ReadLengthReadFilter 2019-11-23T22:48:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036734911-CleanSam-Picard 2019-11-23T22:48:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799331-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T15:43:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799351-ChromosomeCounts 2019-11-25T15:43:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799371-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T15:47:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799391-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T15:48:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799431-OverclippedReadFilter 2019-11-25T15:43:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799451-BwaMemIndexImageCreator 2019-11-25T15:48:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799471-SampleReadFilter 2019-11-25T15:43:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799491-RMSMappingQuality 2019-11-25T15:48:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799511-Funcotator-BETA 2019-11-25T15:48:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799531-CollectQualityYieldMetrics-Picard 2019-11-25T15:43:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799551-CalcMetadataSpark-BETA 2019-11-25T15:48:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799571-SecondOfPairReadFilter 2019-11-25T15:43:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799591-AlignmentAgreesWithHeaderReadFilter 2019-11-25T15:43:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799611-AS-StrandOddsRatio 2019-11-25T15:48:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799631-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T15:48:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799651-AnnotatePairOrientation-BETA 2019-11-25T15:48:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799671-VariantEval-BETA 2019-11-25T15:48:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799691-CountReads 2019-11-25T15:48:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799711-FixVcfHeader-Picard 2019-11-25T15:48:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799731-CollectHsMetrics-Picard 2019-11-25T15:48:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799751-GnarlyGenotyper-BETA 2019-11-25T15:48:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799771-ViewSam-Picard 2019-11-25T15:48:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799791-CountVariants 2019-11-25T15:48:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799811-AllowAllReadsReadFilter 2019-11-25T15:44:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799831-LiftOverIntervalList-Picard 2019-11-25T15:44:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799851-BamToBfq-Picard 2019-11-25T15:44:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799871-PrimaryLineReadFilter 2019-11-25T15:44:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799891-CollectMultipleMetricsSpark-BETA 2019-11-25T15:48:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799911-FindBreakpointEvidenceSpark-BETA 2019-11-25T15:48:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799931-UniqueAltReadCount 2019-11-25T15:44:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799951-QualByDepth 2019-11-25T15:48:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799971-NormalizeFasta-Picard 2019-11-25T15:48:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036799991-IlluminaBasecallsToFastq-Picard 2019-11-25T15:48:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800011-SamFormatConverter-Picard 2019-11-25T15:44:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800051-FisherStrand 2019-11-25T15:48:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800071-ClusterCrosscheckMetrics-Picard 2019-11-25T15:44:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800091-SoftClippedReadFilter 2019-11-25T15:44:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800111-GetSampleName-BETA 2019-11-25T15:48:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800131-MarkDuplicatesSpark-BETA 2019-11-25T15:48:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800151-DepthPerAlleleBySample 2019-11-25T15:48:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800171-CalculateReadGroupChecksum-Picard 2019-11-25T15:48:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800191-SetNmMdAndUqTags-Picard 2019-11-25T15:48:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800211-FuncotateSegments-BETA 2019-11-25T15:48:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800231-AS-FisherStrand 2019-11-25T15:48:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800251-CompareBaseQualities 2019-11-25T15:44:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800271-CollectAlignmentSummaryMetrics-Picard 2019-11-25T15:44:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800291-CollectSequencingArtifactMetrics-Picard 2019-11-25T15:44:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800311-MappedReadFilter 2019-11-25T15:44:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800331-MarkDuplicatesWithMateCigar-Picard 2019-11-25T15:48:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800351-GatherBQSRReports 2019-11-25T15:44:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800371-ApplyBQSR 2019-11-25T15:48:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800391-CpxVariantReInterpreterSpark-BETA 2019-11-25T15:48:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800411-MakeSitesOnlyVcf-Picard 2019-11-25T15:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800431-CollectInsertSizeMetrics-Picard 2019-11-25T15:44:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800451-MappingQualityRankSumTest 2019-11-25T15:48:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800471-MappingQualityNotZeroReadFilter 2019-11-25T15:45:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800491-NonNFastaSize-Picard 2019-11-25T15:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800511-CalculateMixingFractions 2019-11-25T15:48:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800531-CollectQualityYieldMetricsSpark-BETA 2019-11-25T15:49:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800551-CreateHadoopBamSplittingIndex-BETA 2019-11-25T15:49:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800571-PrintReads 2019-11-25T15:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800591-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T15:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800611-HaplotypeCaller 2019-11-25T15:49:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800631-MateUnmappedAndUnmappedReadFilter 2019-11-25T15:45:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800651-CollectIlluminaLaneMetrics-Picard 2019-11-25T15:49:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800671-CountBasesInReference 2019-11-25T15:49:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800691-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T15:45:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800711-MarkIlluminaAdapters-Picard 2019-11-25T15:49:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800731-SampleList 2019-11-25T15:45:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800751-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T15:49:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800771-FragmentLength 2019-11-25T15:45:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800791-CollectTargetedPcrMetrics-Picard 2019-11-25T15:49:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800811-ReblockGVCF-EXPERIMENTAL 2019-11-25T15:49:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800831-MergeBamAlignment-Picard 2019-11-25T15:45:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800851-LeftAlignAndTrimVariants 2019-11-25T15:49:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800871-ModelSegments-BETA 2019-11-25T15:45:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800891-ExtractIlluminaBarcodes-Picard 2019-11-25T15:49:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800911-AmbiguousBaseReadFilter 2019-11-25T15:45:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800931-CompareDuplicatesSpark-BETA 2019-11-25T15:49:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800951-CollectRawWgsMetrics-Picard 2019-11-25T15:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800971-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T15:49:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036800991-MarkDuplicates-Picard 2019-11-25T15:49:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801011-GenotypeSummaries 2019-11-25T15:45:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801031-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T15:49:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801051-CollectWgsMetrics-Picard 2019-11-25T15:49:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801071-GetPileupSummaries-BETA 2019-11-25T15:49:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801091-FifoBuffer-Picard 2019-11-25T15:46:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801111-VariantFiltration 2019-11-25T15:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801131-LikelihoodRankSumTest 2019-11-25T15:46:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801151-BaseRecalibrator 2019-11-25T15:49:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801171-RevertBaseQualityScores 2019-11-25T15:49:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801191-ClippingRankSumTest 2019-11-25T15:46:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801211-CompareSAMs-Picard 2019-11-25T15:49:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801231-BQSRPipelineSpark-BETA 2019-11-25T15:49:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801251-PossibleDeNovo 2019-11-25T15:46:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801271-DenoiseReadCounts-BETA 2019-11-25T15:46:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801291-BaseQualityRankSumTest 2019-11-25T15:46:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801311-IntervalListToBed-Picard 2019-11-25T15:46:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801331-GermlineCNVCaller-BETA 2019-11-25T15:46:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801351-CallCopyRatioSegments-BETA 2019-11-25T15:46:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801371-AS-InbreedingCoeff 2019-11-25T15:49:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801391-PlatformReadFilter 2019-11-25T15:46:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801411-BamIndexStats-Picard 2019-11-25T15:49:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801431-FilterMutectCalls 2019-11-25T15:49:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801451-VcfFormatConverter-Picard 2019-11-25T15:49:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801471-AddOrReplaceReadGroups-Picard 2019-11-25T15:46:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801491-CollectVariantCallingMetrics-Picard 2019-11-25T15:46:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801511-CombineGVCFs 2019-11-25T15:49:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801531-CollectGcBiasMetrics-Picard 2019-11-25T15:46:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801551-ReadPosition 2019-11-25T15:46:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801571-Coverage 2019-11-25T15:50:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801591-ApplyBQSRSpark-BETA 2019-11-25T15:50:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801611-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T15:50:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801631-PreprocessIntervals-BETA 2019-11-25T15:50:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801651-QualityScoreDistribution-Picard 2019-11-25T15:46:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801671-InbreedingCoeff 2019-11-25T15:46:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801691-FixMateInformation-Picard 2019-11-25T15:46:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801711-PrintVariantsSpark-BETA 2019-11-25T15:50:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801731-ValidateSamFile-Picard 2019-11-25T15:50:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801751-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T15:46:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801771-FuncotatorDataSourceDownloader-BETA 2019-11-25T15:46:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801791-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T15:46:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801811-MergeSamFiles-Picard 2019-11-25T15:50:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801831-CollectRnaSeqMetrics-Picard 2019-11-25T15:46:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801851-GatherVcfsCloud-BETA 2019-11-25T15:50:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801871-PathSeqScoreSpark 2019-11-25T15:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801891-SplitReads 2019-11-25T15:50:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801911-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T15:50:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801931-IntervalOverlapReadFilter 2019-11-25T15:47:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801951-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T15:47:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801971-VariantRecalibrator 2019-11-25T15:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036801991-PathSeqFilterSpark 2019-11-25T15:50:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802011-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T15:50:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802031-SplitIntervals 2019-11-25T15:50:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802051-FastaAlternateReferenceMaker 2019-11-25T15:50:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802071-EvaluateInfoFieldConcordance-BETA 2019-11-25T15:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802091-NonZeroFragmentLengthReadFilter 2019-11-25T15:47:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802131-ProperlyPairedReadFilter 2019-11-25T15:47:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802151-CNNVariantTrain-EXPERIMENTAL 2019-11-25T15:50:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802171-TandemRepeat 2019-11-25T15:47:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802191-FindBadGenomicKmersSpark-BETA 2019-11-25T15:50:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802211-AddCommentsToBam-Picard 2019-11-25T15:50:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802231-AnalyzeSaturationMutagenesis-BETA 2019-11-25T15:50:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802251-AS-BaseQualityRankSumTest 2019-11-25T15:50:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802271-Concordance-BETA 2019-11-25T15:50:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802291-FragmentLengthReadFilter 2019-11-25T15:47:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802311-NotSecondaryAlignmentReadFilter 2019-11-25T15:47:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802331-FindMendelianViolations-Picard 2019-11-25T15:50:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802351-IndexFeatureFile 2019-11-25T15:47:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802371-MetricsReadFilter 2019-11-25T15:47:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802391-ValidAlignmentEndReadFilter 2019-11-25T15:50:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802411-FastaReferenceMaker 2019-11-25T15:50:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802431-DepthPerSampleHC 2019-11-25T15:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802451-AlleleFraction 2019-11-25T15:50:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802471-OrientationBiasReadCounts 2019-11-25T15:47:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802491-CountNs 2019-11-25T15:47:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802511-RenameSampleInVcf-Picard 2019-11-25T15:50:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802531-MappingQualityAvailableReadFilter 2019-11-25T15:47:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802551-CollectOxoGMetrics-Picard 2019-11-25T15:47:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802571-CreateReadCountPanelOfNormals-BETA 2019-11-25T15:47:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802591-CountReadsSpark-BETA 2019-11-25T15:50:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802611-PrintReadsSpark-BETA 2019-11-25T15:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802631-FilterVariantTranches-EXPERIMENTAL 2019-11-25T15:50:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802651-CheckTerminatorBlock-Picard 2019-11-25T15:47:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802671-ReadLengthReadFilter 2019-11-25T15:47:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802771-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T15:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802791-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T15:57:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802811-NonChimericOriginalAlignmentReadFilter 2019-11-25T15:52:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802831-MeanQualityByCycle-Picard 2019-11-25T15:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802851-GenotypeConcordance-Picard 2019-11-25T15:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802871-Pileup 2019-11-25T15:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802891-WellformedReadFilter 2019-11-25T15:57:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802911-SampleReadFilter 2019-11-25T15:52:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802931-AnalyzeCovariates 2019-11-25T15:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802951-FirstOfPairReadFilter 2019-11-25T15:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802971-CollectQualityYieldMetrics-Picard 2019-11-25T15:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036802991-PathSeqPipelineSpark 2019-11-25T15:57:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803011-AlignmentAgreesWithHeaderReadFilter 2019-11-25T15:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803031-AS-StrandOddsRatio 2019-11-25T15:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803051-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T15:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803071-AnnotatePairOrientation-BETA 2019-11-25T15:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803091-VariantEval-BETA 2019-11-25T15:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803111-CollectHsMetrics-Picard 2019-11-25T15:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803131-GnarlyGenotyper-BETA 2019-11-25T15:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803151-EstimateLibraryComplexity-Picard 2019-11-25T15:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803171-ViewSam-Picard 2019-11-25T15:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803191-AllowAllReadsReadFilter 2019-11-25T15:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803211-LiftOverIntervalList-Picard 2019-11-25T15:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803231-BamToBfq-Picard 2019-11-25T15:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803251-CollectMultipleMetricsSpark-BETA 2019-11-25T15:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803271-NormalizeFasta-Picard 2019-11-25T15:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803291-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T15:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803311-UpdateVCFSequenceDictionary 2019-11-25T15:57:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803331-FisherStrand 2019-11-25T15:57:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803351-ClusterCrosscheckMetrics-Picard 2019-11-25T15:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803371-ClipReads 2019-11-25T15:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803391-CollectSamErrorMetrics-Picard 2019-11-25T15:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803411-MarkDuplicatesSpark-BETA 2019-11-25T15:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803431-SetNmMdAndUqTags-Picard 2019-11-25T15:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803451-CalculateFingerprintMetrics-Picard 2019-11-25T15:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803471-PathSeqBuildReferenceTaxonomy 2019-11-25T15:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803491-CompareBaseQualities 2019-11-25T15:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803511-BwaSpark-BETA 2019-11-25T15:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803531-CollectAlignmentSummaryMetrics-Picard 2019-11-25T15:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803551-CollectSequencingArtifactMetrics-Picard 2019-11-25T15:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803571-GatherVcfs-Picard 2019-11-25T15:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803611-GatherBQSRReports 2019-11-25T15:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803631-PathSeqBuildKmers 2019-11-25T15:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803651-MakeSitesOnlyVcf-Picard 2019-11-25T15:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803671-CollectReadCounts-BETA 2019-11-25T15:58:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803691-MappingQualityRankSumTest 2019-11-25T15:58:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803711-MappingQualityNotZeroReadFilter 2019-11-25T15:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803731-CollectJumpingLibraryMetrics-Picard 2019-11-25T15:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803751-SplitSamByNumberOfReads-Picard 2019-11-25T15:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803771-MateDifferentStrandReadFilter 2019-11-25T15:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803791-NonNFastaSize-Picard 2019-11-25T15:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803911-GenomicsDBImport 2019-11-25T15:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803931-OxoGReadCounts 2019-11-25T15:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803951-CreateHadoopBamSplittingIndex-BETA 2019-11-25T15:58:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803971-CrosscheckReadGroupFingerprints-Picard 2019-11-25T15:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036803991-HaplotypeCaller 2019-11-25T15:58:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804011-ReadsPipelineSpark-BETA 2019-11-25T15:58:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804031-ReplaceSamHeader-Picard 2019-11-25T15:58:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804051-CountFalsePositives-BETA 2019-11-25T15:58:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804071-MateUnmappedAndUnmappedReadFilter 2019-11-25T15:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804091-CountBasesInReference 2019-11-25T15:58:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804111-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T15:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804131-SetNmAndUqTags-Picard 2019-11-25T15:58:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804151-PathSeqBwaSpark 2019-11-25T15:58:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804171-MarkIlluminaAdapters-Picard 2019-11-25T15:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804191-MatchingBasesAndQualsReadFilter 2019-11-25T15:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804231-FragmentLength 2019-11-25T15:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804251-CheckIlluminaDirectory-Picard 2019-11-25T15:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804271-CollectBaseDistributionByCycle-Picard 2019-11-25T15:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804291-ReblockGVCF-EXPERIMENTAL 2019-11-25T15:58:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804311-MergeBamAlignment-Picard 2019-11-25T15:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804331-LeftAlignAndTrimVariants 2019-11-25T15:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804351-ModelSegments-BETA 2019-11-25T15:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804371-ExtractIlluminaBarcodes-Picard 2019-11-25T15:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804411-BedToIntervalList-Picard 2019-11-25T15:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804431-RemoveNearbyIndels 2019-11-25T15:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804451-CompareDuplicatesSpark-BETA 2019-11-25T15:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804471-CollectRawWgsMetrics-Picard 2019-11-25T15:58:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804491-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T15:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804511-MarkDuplicates-Picard 2019-11-25T15:58:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804531-VcfToAdpc-Picard 2019-11-25T15:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804551-GoodCigarReadFilter 2019-11-25T15:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804571-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T15:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804591-PositionBasedDownsampleSam-Picard 2019-11-25T15:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804611-PostprocessGermlineCNVCalls-BETA 2019-11-25T15:58:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804631-GenotypeSummaries 2019-11-25T15:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804651-FlagStatSpark-BETA 2019-11-25T15:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804671-CollectWgsMetrics-Picard 2019-11-25T15:58:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804691-FifoBuffer-Picard 2019-11-25T15:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804711-ExcessHet 2019-11-25T15:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804771-RevertBaseQualityScores 2019-11-25T15:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804851-GatherTranches-BETA 2019-11-25T15:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804871-DownsampleSam-Picard 2019-11-25T15:58:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804891-ClippingRankSumTest 2019-11-25T15:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804911-CompareSAMs-Picard 2019-11-25T15:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804931-EstimateLibraryComplexityGATK-BETA 2019-11-25T15:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804951-CollectInsertSizeMetricsSpark-BETA 2019-11-25T15:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804971-BaseQualityRankSumTest 2019-11-25T15:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036804991-ApplyVQSR 2019-11-25T15:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805011-UpdateVcfSequenceDictionary-Picard 2019-11-25T15:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805031-ReadNameReadFilter 2019-11-25T15:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805051-CallCopyRatioSegments-BETA 2019-11-25T15:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805071-ScatterIntervalsByNs-Picard 2019-11-25T15:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805091-AS-InbreedingCoeff 2019-11-25T15:59:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805111-FilterMutectCalls 2019-11-25T15:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805131-VcfFormatConverter-Picard 2019-11-25T15:59:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805151-PlotModeledSegments-BETA 2019-11-25T15:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805171-CollectVariantCallingMetrics-Picard 2019-11-25T15:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805191-CombineGVCFs 2019-11-25T15:59:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805211-ReadPosition 2019-11-25T15:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805231-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T15:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805251-ReadStrandFilter 2019-11-25T15:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805271-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T15:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805291-CalculateGenotypePosteriors 2019-11-25T15:59:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805311-CollectMultipleMetrics-Picard 2019-11-25T15:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805331-ExtractSVEvidenceSpark-BETA 2019-11-25T15:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805351-CNNScoreVariants-EXPERIMENTAL 2019-11-25T15:59:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805371-PreprocessIntervals-BETA 2019-11-25T15:59:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805391-FlagStat 2019-11-25T15:59:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805411-PrintVariantsSpark-BETA 2019-11-25T15:59:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805431-ValidateSamFile-Picard 2019-11-25T15:59:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805451-ReadGroupBlackListReadFilter 2019-11-25T15:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805471-SamToFastq-Picard 2019-11-25T15:59:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805491-SortSam-Picard 2019-11-25T15:59:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805511-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T15:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805531-FuncotatorDataSourceDownloader-BETA 2019-11-25T15:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805551-StrandArtifact 2019-11-25T15:56:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805571-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T15:56:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805591-MergeSamFiles-Picard 2019-11-25T15:59:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805611-GatherVcfsCloud-BETA 2019-11-25T15:59:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805631-PathSeqScoreSpark 2019-11-25T15:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805651-BaseQuality 2019-11-25T15:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805671-SeqIsStoredReadFilter 2019-11-25T15:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805711-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T15:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805811-VariantRecalibrator 2019-11-25T15:59:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805831-PathSeqFilterSpark 2019-11-25T15:59:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805851-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T15:59:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805871-SplitIntervals 2019-11-25T15:59:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805891-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T15:59:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805911-EvaluateInfoFieldConcordance-BETA 2019-11-25T15:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805931-SplitNCigarReads 2019-11-25T15:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805951-SplitSamByLibrary-Picard 2019-11-25T15:59:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805971-CrosscheckFingerprints-Picard 2019-11-25T15:59:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036805991-CNNVariantTrain-EXPERIMENTAL 2019-11-25T15:59:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806011-GenotypeGVCFs 2019-11-25T15:59:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806031-TandemRepeat 2019-11-25T15:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806051-AS-QualByDepth 2019-11-25T15:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806071-FragmentLengthReadFilter 2019-11-25T15:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806091-NotSecondaryAlignmentReadFilter 2019-11-25T15:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806111-FindMendelianViolations-Picard 2019-11-25T15:59:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806131-IndexFeatureFile 2019-11-25T15:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806151-MetricsReadFilter 2019-11-25T15:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806171-QualityScoreDistributionSpark-BETA 2019-11-25T15:59:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806191-DepthPerSampleHC 2019-11-25T15:59:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806211-AlleleFraction 2019-11-25T15:59:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806231-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T15:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806251-OrientationBiasReadCounts 2019-11-25T15:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806271-CountNs 2019-11-25T15:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806291-MappingQualityAvailableReadFilter 2019-11-25T15:56:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806311-CountReadsSpark-BETA 2019-11-25T16:00:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806331-CountBasesSpark-BETA 2019-11-25T16:00:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806351-PrintReadsSpark-BETA 2019-11-25T16:00:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806371-FilterVariantTranches-EXPERIMENTAL 2019-11-25T16:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806391-CreateSomaticPanelOfNormals-BETA 2019-11-25T16:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806411-CheckPileup 2019-11-25T16:00:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806431-GtcToVcf-Picard 2019-11-25T15:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806451-ReadLengthReadFilter 2019-11-25T15:57:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036806471-CleanSam-Picard 2019-11-25T15:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817391-LibraryReadFilter 2019-11-25T18:21:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817411-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T18:25:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817431-MeanQualityByCycle-Picard 2019-11-25T18:25:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817451-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T18:25:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817471-GenotypeConcordance-Picard 2019-11-25T18:25:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817491-OverclippedReadFilter 2019-11-25T18:21:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817511-SampleReadFilter 2019-11-25T18:21:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817531-RMSMappingQuality 2019-11-25T18:25:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817551-FirstOfPairReadFilter 2019-11-25T18:21:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817571-PathSeqPipelineSpark 2019-11-25T18:25:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817591-CalcMetadataSpark-BETA 2019-11-25T18:25:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817611-AS-StrandOddsRatio 2019-11-25T18:25:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817631-FilterVcf-Picard 2019-11-25T18:21:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817651-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T18:25:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817671-VariantEval-BETA 2019-11-25T18:25:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817691-FixVcfHeader-Picard 2019-11-25T18:25:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817711-CollectHsMetrics-Picard 2019-11-25T18:25:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817731-EstimateLibraryComplexity-Picard 2019-11-25T18:25:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817751-ViewSam-Picard 2019-11-25T18:25:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817771-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T18:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817791-CountVariants 2019-11-25T18:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817811-AllowAllReadsReadFilter 2019-11-25T18:21:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817831-LiftOverIntervalList-Picard 2019-11-25T18:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817851-NotDuplicateReadFilter 2019-11-25T18:21:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817871-PrimaryLineReadFilter 2019-11-25T18:21:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817891-CollectMultipleMetricsSpark-BETA 2019-11-25T18:25:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817911-StrandOddsRatio 2019-11-25T18:25:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817931--Tool-Documentation-Index 2019-12-16T20:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817951-CheckFingerprint-Picard 2019-11-25T18:21:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817971-HasReadGroupReadFilter 2019-11-25T18:21:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036817991-DetermineGermlineContigPloidy-BETA 2019-11-25T18:21:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818011-FindBreakpointEvidenceSpark-BETA 2019-11-25T18:25:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818031-MappingQuality 2019-11-25T18:21:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818051-QualByDepth 2019-11-25T18:25:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818071-VariantsToTable 2019-11-25T18:25:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818091-NormalizeFasta-Picard 2019-11-25T18:25:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818111-AS-RMSMappingQuality 2019-11-25T18:25:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818131-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T18:25:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818151-IlluminaBasecallsToFastq-Picard 2019-11-25T18:25:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818171-FisherStrand 2019-11-25T18:25:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818191-ClipReads 2019-11-25T18:25:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818211-CollectSamErrorMetrics-Picard 2019-11-25T18:21:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818231-CalculateReadGroupChecksum-Picard 2019-11-25T18:25:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818251-SetNmMdAndUqTags-Picard 2019-11-25T18:25:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818271-FuncotateSegments-BETA 2019-11-25T18:25:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818291-GatherBamFiles-Picard 2019-11-25T18:22:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818311-BwaSpark-BETA 2019-11-25T18:25:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818331-CollectAlignmentSummaryMetrics-Picard 2019-11-25T18:22:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818371-GatherVcfs-Picard 2019-11-25T18:22:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818391-MappedReadFilter 2019-11-25T18:22:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818411-MarkDuplicatesWithMateCigar-Picard 2019-11-25T18:25:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818431-IntervalListTools-Picard 2019-11-25T18:26:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818451-CollectInsertSizeMetrics-Picard 2019-11-25T18:22:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818471-StrandBiasBySample 2019-11-25T18:26:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818491-FilterIntervals 2019-11-25T18:22:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818511-MappingQualityRankSumTest 2019-11-25T18:26:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818531-FilterMutectCalls 2019-11-25T18:26:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818551-IlluminaBasecallsToSam-Picard 2019-11-25T18:26:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818571-MappingQualityReadFilter 2019-11-25T18:26:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818611-PlatformUnitReadFilter 2019-11-25T18:22:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818631-OxoGReadCounts 2019-11-25T18:22:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818651-CreateHadoopBamSplittingIndex-BETA 2019-11-25T18:26:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818671-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T18:26:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818691-HaplotypeCaller 2019-11-25T18:26:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818711-ValidAlignmentStartReadFilter 2019-11-25T18:26:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818731-CountFalsePositives-BETA 2019-11-25T18:26:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818751-MateUnmappedAndUnmappedReadFilter 2019-11-25T18:22:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818771-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T18:22:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818791-SetNmAndUqTags-Picard 2019-11-25T18:26:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818811-PathSeqBwaSpark 2019-11-25T18:26:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818831-SampleList 2019-11-25T18:22:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818851-MatchingBasesAndQualsReadFilter 2019-11-25T18:22:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818871-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T18:26:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818891-MeanQualityByCycleSpark-BETA 2019-11-25T18:26:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818911-CheckIlluminaDirectory-Picard 2019-11-25T18:26:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818931-CollectTargetedPcrMetrics-Picard 2019-11-25T18:26:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818951-ReblockGVCF-EXPERIMENTAL 2019-11-25T18:26:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818971-MergeBamAlignment-Picard 2019-11-25T18:22:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036818991-ExtractIlluminaBarcodes-Picard 2019-11-25T18:26:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819011-AmbiguousBaseReadFilter 2019-11-25T18:23:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819031-BedToIntervalList-Picard 2019-11-25T18:26:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819051-CompareDuplicatesSpark-BETA 2019-11-25T18:26:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819071-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T18:26:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819091-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T18:26:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819111-OriginalAlignment 2019-11-25T18:23:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819131-MarkDuplicates-Picard 2019-11-25T18:26:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819151-CreateSequenceDictionary-Picard 2019-11-25T18:26:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819171-GoodCigarReadFilter 2019-11-25T18:23:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819191-ReorderSam-Picard 2019-11-25T18:23:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819211-PostprocessGermlineCNVCalls-BETA 2019-11-25T18:26:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819231-GenotypeSummaries 2019-11-25T18:23:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819251-FlagStatSpark-BETA 2019-11-25T18:26:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819271-CollectWgsMetrics-Picard 2019-11-25T18:26:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819291-AS-ReadPosRankSumTest 2019-11-25T18:26:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819311-FifoBuffer-Picard 2019-11-25T18:23:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819331-ExcessHet 2019-11-25T18:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819351-VariantFiltration 2019-11-25T18:26:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819371-BaseRecalibrator 2019-11-25T18:26:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819431-CompareSAMs-Picard 2019-11-25T18:26:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819451-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:26:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819471-CollectInsertSizeMetricsSpark-BETA 2019-11-25T18:26:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819491-DenoiseReadCounts-BETA 2019-11-25T18:23:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819511-BaseQualityRankSumTest 2019-11-25T18:23:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819531-ApplyVQSR 2019-11-25T18:26:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819551-GermlineCNVCaller-BETA 2019-11-25T18:23:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819571-UpdateVcfSequenceDictionary-Picard 2019-11-25T18:23:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819591-MappingQualityZero 2019-11-25T18:26:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819611-BamIndexStats-Picard 2019-11-25T18:27:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819631-Mutect2 2019-11-25T18:27:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819651-VcfFormatConverter-Picard 2019-11-25T18:27:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819671-AddOrReplaceReadGroups-Picard 2019-11-25T18:23:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819691-PlotModeledSegments-BETA 2019-11-25T18:23:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819731-ReadPosition 2019-11-25T18:23:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819751-Coverage 2019-11-25T18:27:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819771-ReadStrandFilter 2019-11-25T18:23:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819791-ApplyBQSRSpark-BETA 2019-11-25T18:27:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819811-CollectAllelicCounts-BETA 2019-11-25T18:27:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819831-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T18:24:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819851-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T18:27:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819871-PreprocessIntervals-BETA 2019-11-25T18:27:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819891-InbreedingCoeff 2019-11-25T18:24:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819911-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T18:27:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819931-SortVcf-Picard 2019-11-25T18:27:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819951-ValidateSamFile-Picard 2019-11-25T18:27:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819971-FastqToSam-Picard 2019-11-25T18:27:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036819991-ReadGroupBlackListReadFilter 2019-11-25T18:24:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820011-SamToFastq-Picard 2019-11-25T18:27:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820031-SortSam-Picard 2019-11-25T18:27:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820051-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T18:24:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820071-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T18:24:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820091-MergeSamFiles-Picard 2019-11-25T18:27:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820111-GatherVcfsCloud-BETA 2019-11-25T18:27:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820131-AnnotateIntervals-BETA 2019-11-25T18:27:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820151-RevertSam-Picard 2019-11-25T18:27:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820171-PassesVendorQualityCheckReadFilter 2019-11-25T18:24:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820191-SplitReads 2019-11-25T18:27:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820211-ReadPosRankSumTest 2019-11-25T18:24:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820231-BaseQuality 2019-11-25T18:24:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820251-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T18:24:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820271-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T18:27:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820291-PathSeqFilterSpark 2019-11-25T18:27:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820311-PlotDenoisedCopyRatios-BETA 2019-11-25T18:24:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820331-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T18:27:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820351-ProperlyPairedReadFilter 2019-11-25T18:24:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820371-SplitVcfs-Picard 2019-11-25T18:27:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820391-SplitSamByLibrary-Picard 2019-11-25T18:27:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820411-CNNVariantTrain-EXPERIMENTAL 2019-11-25T18:27:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820431-GenotypeGVCFs 2019-11-25T18:27:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820451-TandemRepeat 2019-11-25T18:24:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820471-AnalyzeSaturationMutagenesis-BETA 2019-11-25T18:27:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820491-AS-BaseQualityRankSumTest 2019-11-25T18:27:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820511-FragmentLengthReadFilter 2019-11-25T18:24:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820531-CollectRrbsMetrics-Picard 2019-11-25T18:24:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820551-NotSecondaryAlignmentReadFilter 2019-11-25T18:24:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820571-ReferenceBases 2019-11-25T18:24:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820591-IndexFeatureFile 2019-11-25T18:24:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820611-MetricsReadFilter 2019-11-25T18:24:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820631-QualityScoreDistributionSpark-BETA 2019-11-25T18:27:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820651-DepthPerSampleHC 2019-11-25T18:27:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820671-AlleleFraction 2019-11-25T18:27:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820711-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T18:25:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820751-CountNs 2019-11-25T18:25:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820771-RenameSampleInVcf-Picard 2019-11-25T18:27:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820791-MappingQualityAvailableReadFilter 2019-11-25T18:25:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820811-CollectOxoGMetrics-Picard 2019-11-25T18:25:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820831-CreateReadCountPanelOfNormals-BETA 2019-11-25T18:25:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820851-CountReadsSpark-BETA 2019-11-25T18:27:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820871-CountBasesSpark-BETA 2019-11-25T18:28:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820891-PrintReadsSpark-BETA 2019-11-25T18:28:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820911-FilterVariantTranches-EXPERIMENTAL 2019-11-25T18:28:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820931-CheckPileup 2019-11-25T18:28:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820951-GtcToVcf-Picard 2019-11-25T18:25:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820971-CheckTerminatorBlock-Picard 2019-11-25T18:25:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036820991-ReadLengthReadFilter 2019-11-25T18:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821011-CleanSam-Picard 2019-11-25T18:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821351-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T18:32:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821371-ChromosomeCounts 2019-11-25T18:32:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821391-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T18:36:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821411-MeanQualityByCycle-Picard 2019-11-25T18:36:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821431-GenotypeConcordance-Picard 2019-11-25T18:36:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821451-Pileup 2019-11-25T18:36:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821471-BwaMemIndexImageCreator 2019-11-25T18:36:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821491-WellformedReadFilter 2019-11-25T18:36:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821511-SampleReadFilter 2019-11-25T18:32:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821531-AnalyzeCovariates 2019-11-25T18:36:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821551-RMSMappingQuality 2019-11-25T18:36:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821571-PathSeqPipelineSpark 2019-11-25T18:36:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821591-CalcMetadataSpark-BETA 2019-11-25T18:36:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821611-AS-StrandOddsRatio 2019-11-25T18:36:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821631-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T18:36:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821651-VariantEval-BETA 2019-11-25T18:36:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821691-CountReads 2019-11-25T18:36:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821711-FixVcfHeader-Picard 2019-11-25T18:36:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821751-ViewSam-Picard 2019-11-25T18:36:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821771-AllowAllReadsReadFilter 2019-11-25T18:33:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821791-VariantAnnotator-BETA 2019-11-25T18:36:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821811-FilterSamReads-Picard 2019-11-25T18:36:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821831-CountBases 2019-11-25T18:36:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821851--Tool-Documentation-Index 2019-12-16T20:19:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821871-CheckFingerprint-Picard 2019-11-25T18:33:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821891-UniqueAltReadCount 2019-11-25T18:33:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821911-MappingQuality 2019-11-25T18:33:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821931-QualByDepth 2019-11-25T18:37:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821971-NormalizeFasta-Picard 2019-11-25T18:37:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036821991-AS-RMSMappingQuality 2019-11-25T18:37:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822011-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T18:37:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822031-CountVariantsSpark-BETA 2019-11-25T18:37:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822051-UpdateVCFSequenceDictionary 2019-11-25T18:37:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822071-ClusterCrosscheckMetrics-Picard 2019-11-25T18:33:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822091-ClipReads 2019-11-25T18:37:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822111-CollectSamErrorMetrics-Picard 2019-11-25T18:33:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822131-DepthPerAlleleBySample 2019-11-25T18:37:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822151-FuncotateSegments-BETA 2019-11-25T18:37:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822171-GatherBamFiles-Picard 2019-11-25T18:33:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822191-AS-FisherStrand 2019-11-25T18:37:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822211-CollectAlignmentSummaryMetrics-Picard 2019-11-25T18:33:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822231-CollectSequencingArtifactMetrics-Picard 2019-11-25T18:33:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822251-MarkDuplicatesWithMateCigar-Picard 2019-11-25T18:37:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822271-MakeSitesOnlyVcf-Picard 2019-11-25T18:37:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822291-CollectInsertSizeMetrics-Picard 2019-11-25T18:33:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822311-StrandBiasBySample 2019-11-25T18:37:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822331-SortSamSpark-BETA 2019-11-25T18:37:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822351-FilterIntervals 2019-11-25T18:33:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822371-SplitSamByNumberOfReads-Picard 2019-11-25T18:37:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822391-MateDifferentStrandReadFilter 2019-11-25T18:37:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822411-NonNFastaSize-Picard 2019-11-25T18:37:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822431-FilterMutectCalls 2019-11-25T18:37:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822451-BaseRecalibratorSpark-BETA 2019-11-25T18:37:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822471-CalculateMixingFractions 2019-11-25T18:37:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822491-SelectVariants 2019-11-25T18:37:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822511-AccumulateVariantCallingMetrics-Picard 2019-11-25T18:33:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822531-ReadGroupReadFilter 2019-11-25T18:33:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822551-MappingQualityReadFilter 2019-11-25T18:37:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822571-CollectQualityYieldMetricsSpark-BETA 2019-11-25T18:37:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822591-PlatformUnitReadFilter 2019-11-25T18:34:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822611-CreateHadoopBamSplittingIndex-BETA 2019-11-25T18:37:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822631-CrosscheckReadGroupFingerprints-Picard 2019-11-25T18:34:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822651-ValidAlignmentStartReadFilter 2019-11-25T18:37:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822671-ReadsPipelineSpark-BETA 2019-11-25T18:37:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822691-ReplaceSamHeader-Picard 2019-11-25T18:37:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822711-MateUnmappedAndUnmappedReadFilter 2019-11-25T18:34:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822731-CollectIlluminaLaneMetrics-Picard 2019-11-25T18:37:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822751-VcfToIntervalList-Picard 2019-11-25T18:37:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822771-SetNmAndUqTags-Picard 2019-11-25T18:37:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822791-MarkIlluminaAdapters-Picard 2019-11-25T18:37:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822811-SampleList 2019-11-25T18:34:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822831-MatchingBasesAndQualsReadFilter 2019-11-25T18:34:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822851-MeanQualityByCycleSpark-BETA 2019-11-25T18:37:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822871-CollectTargetedPcrMetrics-Picard 2019-11-25T18:37:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822891-CollectBaseDistributionByCycle-Picard 2019-11-25T18:34:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822911-ReblockGVCF-EXPERIMENTAL 2019-11-25T18:37:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822931-MergeBamAlignment-Picard 2019-11-25T18:34:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822951-FixMisencodedBaseQualityReads 2019-11-25T18:37:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822971-ModelSegments-BETA 2019-11-25T18:34:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036822991-ExtractIlluminaBarcodes-Picard 2019-11-25T18:37:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823011-AmbiguousBaseReadFilter 2019-11-25T18:34:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823031-BedToIntervalList-Picard 2019-11-25T18:37:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823051-CompareDuplicatesSpark-BETA 2019-11-25T18:37:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823071-CollectRawWgsMetrics-Picard 2019-11-25T18:37:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823091-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T18:38:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823111-OriginalAlignment 2019-11-25T18:34:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823131-VcfToAdpc-Picard 2019-11-25T18:34:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823151-GoodCigarReadFilter 2019-11-25T18:34:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823171-ReorderSam-Picard 2019-11-25T18:34:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823191-GenotypeSummaries 2019-11-25T18:34:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823211-PairedReadFilter 2019-11-25T18:34:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823231-AS-ReadPosRankSumTest 2019-11-25T18:38:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823251-FifoBuffer-Picard 2019-11-25T18:34:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823271-ExcessHet 2019-11-25T18:34:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823291-LikelihoodRankSumTest 2019-11-25T18:34:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823311-BaseRecalibrator 2019-11-25T18:38:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823331-GatherTranches-BETA 2019-11-25T18:34:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823351-DownsampleSam-Picard 2019-11-25T18:38:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823371-ClippingRankSumTest 2019-11-25T18:34:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823391-BQSRPipelineSpark-BETA 2019-11-25T18:38:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823411-EstimateLibraryComplexityGATK-BETA 2019-11-25T18:34:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823431-PossibleDeNovo 2019-11-25T18:34:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823451-CollectInsertSizeMetricsSpark-BETA 2019-11-25T18:38:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823471-DenoiseReadCounts-BETA 2019-11-25T18:34:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823491-ApplyVQSR 2019-11-25T18:38:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823511-GermlineCNVCaller-BETA 2019-11-25T18:35:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823531-UpdateVcfSequenceDictionary-Picard 2019-11-25T18:35:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823551-CallCopyRatioSegments-BETA 2019-11-25T18:35:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823571-ScatterIntervalsByNs-Picard 2019-11-25T18:38:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823591-AS-InbreedingCoeff 2019-11-25T18:38:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823631-PlatformReadFilter 2019-11-25T18:35:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823651-BamIndexStats-Picard 2019-11-25T18:38:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823691-LiftoverVcf-Picard 2019-11-25T18:38:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823711-AddOATag-Picard 2019-11-25T18:38:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823731-ReadPosition 2019-11-25T18:35:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823751-Coverage 2019-11-25T18:38:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823771-ReadStrandFilter 2019-11-25T18:35:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823791-ApplyBQSRSpark-BETA 2019-11-25T18:38:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823811-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T18:35:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823831-CalculateGenotypePosteriors 2019-11-25T18:38:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823851-MergeVcfs-Picard 2019-11-25T18:38:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823871-CollectMultipleMetrics-Picard 2019-11-25T18:38:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823891-ValidateVariants 2019-11-25T18:38:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823911-CollectAllelicCounts-BETA 2019-11-25T18:38:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823931-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T18:38:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823951-PreprocessIntervals-BETA 2019-11-25T18:38:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823971-QualityScoreDistribution-Picard 2019-11-25T18:35:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036823991-BaitDesigner-Picard 2019-11-25T18:38:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824031-ValidateSamFile-Picard 2019-11-25T18:38:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824051-ReadGroupBlackListReadFilter 2019-11-25T18:35:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824071-SamToFastq-Picard 2019-11-25T18:38:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824091-SortSam-Picard 2019-11-25T18:38:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824111-FuncotatorDataSourceDownloader-BETA 2019-11-25T18:35:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824131-MergeSamFiles-Picard 2019-11-25T18:38:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824171-AnnotateIntervals-BETA 2019-11-25T18:38:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824191-PathSeqScoreSpark 2019-11-25T18:38:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824231-PassesVendorQualityCheckReadFilter 2019-11-25T18:35:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824251-SplitReads 2019-11-25T18:38:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824271-AS-MappingQualityRankSumTest 2019-11-25T18:38:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824311-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T18:38:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824331-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T18:38:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824351-BaseQuality 2019-11-25T18:35:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824371-SeqIsStoredReadFilter 2019-11-25T18:35:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824391-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T18:38:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824431-UnmarkDuplicates 2019-11-25T18:38:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824451-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T18:38:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824471-SplitNCigarReads 2019-11-25T18:38:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824491-ProperlyPairedReadFilter 2019-11-25T18:36:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824511-CNNVariantTrain-EXPERIMENTAL 2019-11-25T18:39:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824531-GenotypeGVCFs 2019-11-25T18:39:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824551-FindBadGenomicKmersSpark-BETA 2019-11-25T18:39:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824571-AddCommentsToBam-Picard 2019-11-25T18:39:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824591-FragmentLengthReadFilter 2019-11-25T18:36:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824611-BuildBamIndex-Picard 2019-11-25T18:39:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824631-NotSecondaryAlignmentReadFilter 2019-11-25T18:36:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824651-CountNs 2019-11-25T18:36:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824671-CollectOxoGMetrics-Picard 2019-11-25T18:36:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824691-CreateReadCountPanelOfNormals-BETA 2019-11-25T18:36:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824711-CountBasesSpark-BETA 2019-11-25T18:39:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824751-FilterVariantTranches-EXPERIMENTAL 2019-11-25T18:39:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824771-ReadLengthReadFilter 2019-11-25T18:36:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036824791-CleanSam-Picard 2019-11-25T18:36:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825031-ChromosomeCounts 2019-11-25T18:41:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825051-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T18:45:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825071-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T18:45:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825091-GenotypeConcordance-Picard 2019-11-25T18:45:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825111-Pileup 2019-11-25T18:45:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825131-OverclippedReadFilter 2019-11-25T18:41:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825151-BwaMemIndexImageCreator 2019-11-25T18:45:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825171-WellformedReadFilter 2019-11-25T18:45:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825191-SampleReadFilter 2019-11-25T18:41:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825211-FirstOfPairReadFilter 2019-11-25T18:41:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825231-CollectQualityYieldMetrics-Picard 2019-11-25T18:41:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825251-PathSeqPipelineSpark 2019-11-25T18:45:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825271-CalcMetadataSpark-BETA 2019-11-25T18:45:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825291-AS-StrandOddsRatio 2019-11-25T18:45:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825311-FilterVcf-Picard 2019-11-25T18:41:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825331-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T18:45:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825351-AnnotatePairOrientation-BETA 2019-11-25T18:45:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825371-FixVcfHeader-Picard 2019-11-25T18:45:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825391-CollectHsMetrics-Picard 2019-11-25T18:45:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825431-GnarlyGenotyper-BETA 2019-11-25T18:45:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825451-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T18:45:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825471-CountVariants 2019-11-25T18:45:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825491-LiftOverIntervalList-Picard 2019-11-25T18:41:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825511-VariantAnnotator-BETA 2019-11-25T18:45:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825551-FilterSamReads-Picard 2019-11-25T18:45:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825571-CollectMultipleMetricsSpark-BETA 2019-11-25T18:45:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825591--Tool-Documentation-Index 2019-12-16T20:19:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825611-HasReadGroupReadFilter 2019-11-25T18:41:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825631-DetermineGermlineContigPloidy-BETA 2019-11-25T18:41:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825651-FindBreakpointEvidenceSpark-BETA 2019-11-25T18:45:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825671-MappingQuality 2019-11-25T18:41:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825691-UpdateVCFSequenceDictionary 2019-11-25T18:45:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825711-SamFormatConverter-Picard 2019-11-25T18:41:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825731-FisherStrand 2019-11-25T18:45:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825751-ClusterCrosscheckMetrics-Picard 2019-11-25T18:41:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825771-ClipReads 2019-11-25T18:45:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825791-SoftClippedReadFilter 2019-11-25T18:41:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825811-MarkDuplicatesSpark-BETA 2019-11-25T18:45:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825831-DepthPerAlleleBySample 2019-11-25T18:45:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825851-FuncotateSegments-BETA 2019-11-25T18:45:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825871-GatherBamFiles-Picard 2019-11-25T18:41:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825911-AS-FisherStrand 2019-11-25T18:45:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825931-CompareBaseQualities 2019-11-25T18:41:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825951-CollectAlignmentSummaryMetrics-Picard 2019-11-25T18:41:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825971-AnnotateVcfWithBamDepth 2019-11-25T18:45:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036825991-GatherVcfs-Picard 2019-11-25T18:42:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826011-MappedReadFilter 2019-11-25T18:42:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826031-ApplyBQSR 2019-11-25T18:46:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826051-CpxVariantReInterpreterSpark-BETA 2019-11-25T18:46:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826071-PathSeqBuildKmers 2019-11-25T18:46:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826091-IntervalListTools-Picard 2019-11-25T18:46:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826111-SortSamSpark-BETA 2019-11-25T18:46:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826131-LeftAlignIndels 2019-11-25T18:46:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826151-MappingQualityNotZeroReadFilter 2019-11-25T18:42:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826171-CollectJumpingLibraryMetrics-Picard 2019-11-25T18:42:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826191-MateDifferentStrandReadFilter 2019-11-25T18:46:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826211-NonNFastaSize-Picard 2019-11-25T18:46:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826231-FilterMutectCalls 2019-11-25T18:46:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826251-BaseRecalibratorSpark-BETA 2019-11-25T18:46:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826271-SelectVariants 2019-11-25T18:46:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826311-ReadGroupReadFilter 2019-11-25T18:42:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826331-CollectQualityYieldMetricsSpark-BETA 2019-11-25T18:46:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826351-OxoGReadCounts 2019-11-25T18:42:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826371-CreateHadoopBamSplittingIndex-BETA 2019-11-25T18:46:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826391-PrintReads 2019-11-25T18:46:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826411-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T18:46:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826431-HaplotypeCaller 2019-11-25T18:46:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826451-ReadsPipelineSpark-BETA 2019-11-25T18:46:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826471-ReplaceSamHeader-Picard 2019-11-25T18:46:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826491-CountFalsePositives-BETA 2019-11-25T18:46:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826511-CollectIlluminaLaneMetrics-Picard 2019-11-25T18:46:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826531-CountBasesInReference 2019-11-25T18:46:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826551-PolymorphicNuMT 2019-11-25T18:42:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826571-VcfToIntervalList-Picard 2019-11-25T18:46:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826591-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T18:42:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826611-SetNmAndUqTags-Picard 2019-11-25T18:46:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826631-PathSeqBwaSpark 2019-11-25T18:46:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826651-MatchingBasesAndQualsReadFilter 2019-11-25T18:42:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826671-CheckIlluminaDirectory-Picard 2019-11-25T18:46:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826691-CollectTargetedPcrMetrics-Picard 2019-11-25T18:46:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826731-ReblockGVCF-EXPERIMENTAL 2019-11-25T18:46:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826751-MergeBamAlignment-Picard 2019-11-25T18:42:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826771-FixMisencodedBaseQualityReads 2019-11-25T18:46:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826791-LeftAlignAndTrimVariants 2019-11-25T18:46:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826831-RemoveNearbyIndels 2019-11-25T18:46:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826851-CompareDuplicatesSpark-BETA 2019-11-25T18:46:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826871-CollectRawWgsMetrics-Picard 2019-11-25T18:46:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826911-OriginalAlignment 2019-11-25T18:43:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826931-MarkDuplicates-Picard 2019-11-25T18:46:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826951-VcfToAdpc-Picard 2019-11-25T18:43:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036826991-NotSupplementaryAlignmentReadFilter 2019-11-25T18:43:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827011-GenotypeSummaries 2019-11-25T18:43:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827031-FlagStatSpark-BETA 2019-11-25T18:46:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827051-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T18:46:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827071-PairedReadFilter 2019-11-25T18:43:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827091-FifoBuffer-Picard 2019-11-25T18:43:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827111-VariantFiltration 2019-11-25T18:46:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827131-LikelihoodRankSumTest 2019-11-25T18:43:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827171-ClippingRankSumTest 2019-11-25T18:43:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827191-BQSRPipelineSpark-BETA 2019-11-25T18:46:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827231-UpdateVcfSequenceDictionary-Picard 2019-11-25T18:43:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827251-MappingQualityZero 2019-11-25T18:47:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827271-ScatterIntervalsByNs-Picard 2019-11-25T18:47:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827291-AS-InbreedingCoeff 2019-11-25T18:47:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827311-Mutect2 2019-11-25T18:47:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827331-AddOrReplaceReadGroups-Picard 2019-11-25T18:43:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827351-CombineGVCFs 2019-11-25T18:47:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827371-LiftoverVcf-Picard 2019-11-25T18:47:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827391-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T18:47:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827411-ReadStrandFilter 2019-11-25T18:43:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827431-ApplyBQSRSpark-BETA 2019-11-25T18:47:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827451-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T18:43:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827491-ExtractSVEvidenceSpark-BETA 2019-11-25T18:47:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827511-CollectAllelicCounts-BETA 2019-11-25T18:47:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827551-PreprocessIntervals-BETA 2019-11-25T18:47:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827571-FlagStat 2019-11-25T18:47:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827591-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T18:47:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827611-FixMateInformation-Picard 2019-11-25T18:44:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827631-PrintVariantsSpark-BETA 2019-11-25T18:47:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827651-FastqToSam-Picard 2019-11-25T18:47:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827671-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T18:44:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827711-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T18:44:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827731-MergeSamFiles-Picard 2019-11-25T18:47:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827751-CollectRnaSeqMetrics-Picard 2019-11-25T18:44:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827771-GatherVcfsCloud-BETA 2019-11-25T18:47:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827791-AnnotateIntervals-BETA 2019-11-25T18:47:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827811-PathSeqScoreSpark 2019-11-25T18:47:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827831-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T18:47:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827851-ReadPosRankSumTest 2019-11-25T18:44:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827871-SeqIsStoredReadFilter 2019-11-25T18:44:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827911-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T18:47:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827931-PathSeqFilterSpark 2019-11-25T18:47:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827951-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T18:47:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827971-PlotDenoisedCopyRatios-BETA 2019-11-25T18:44:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036827991-SplitIntervals 2019-11-25T18:47:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828031-UnmarkDuplicates 2019-11-25T18:47:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828051-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T18:47:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828071-SplitNCigarReads 2019-11-25T18:47:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828091-NonZeroFragmentLengthReadFilter 2019-11-25T18:44:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828111-PileupSpark-BETA 2019-11-25T18:47:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828131-CigarContainsNoNOperator 2019-11-25T18:44:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828151-SplitVcfs-Picard 2019-11-25T18:47:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828171-SplitSamByLibrary-Picard 2019-11-25T18:47:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828191-CNNVariantTrain-EXPERIMENTAL 2019-11-25T18:47:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828211-GenotypeGVCFs 2019-11-25T18:47:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828231-TandemRepeat 2019-11-25T18:44:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828251-FindBadGenomicKmersSpark-BETA 2019-11-25T18:47:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828271-AnalyzeSaturationMutagenesis-BETA 2019-11-25T18:47:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828291-AS-QualByDepth 2019-11-25T18:47:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828311-AS-BaseQualityRankSumTest 2019-11-25T18:47:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828331-FragmentLengthReadFilter 2019-11-25T18:44:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828351-CollectRrbsMetrics-Picard 2019-11-25T18:44:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828371-FindMendelianViolations-Picard 2019-11-25T18:48:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828391-IndexFeatureFile 2019-11-25T18:44:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828411-FastaReferenceMaker 2019-11-25T18:48:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828431-DepthPerSampleHC 2019-11-25T18:48:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828451-OrientationBiasReadCounts 2019-11-25T18:45:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828471-RenameSampleInVcf-Picard 2019-11-25T18:48:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828491-MappingQualityAvailableReadFilter 2019-11-25T18:45:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828511-CountBasesSpark-BETA 2019-11-25T18:48:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828531-PrintReadsSpark-BETA 2019-11-25T18:48:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828551-ASEReadCounter 2019-11-25T18:48:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828571-FilterVariantTranches-EXPERIMENTAL 2019-11-25T18:48:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828591-CheckPileup 2019-11-25T18:48:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828611-GtcToVcf-Picard 2019-11-25T18:45:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828631-CheckTerminatorBlock-Picard 2019-11-25T18:45:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828651-ReadLengthReadFilter 2019-11-25T18:45:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828951-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T18:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828971-GenotypeConcordance-Picard 2019-11-25T18:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036828991-Pileup 2019-11-25T18:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829011-BwaMemIndexImageCreator 2019-11-25T18:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829031-WellformedReadFilter 2019-11-25T18:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829051-AnalyzeCovariates 2019-11-25T18:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829071-Funcotator-BETA 2019-11-25T18:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829091-PathSeqPipelineSpark 2019-11-25T18:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829111-SecondOfPairReadFilter 2019-11-25T18:51:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829131-AlignmentAgreesWithHeaderReadFilter 2019-11-25T18:51:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829151-AS-StrandOddsRatio 2019-11-25T18:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829171-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T18:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829191-AnnotatePairOrientation-BETA 2019-11-25T18:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829211-VariantEval-BETA 2019-11-25T18:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829231-CountReads 2019-11-25T18:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829251-CollectHsMetrics-Picard 2019-11-25T18:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829271-AllowAllReadsReadFilter 2019-11-25T18:51:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829291-LiftOverIntervalList-Picard 2019-11-25T18:51:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829331-NotDuplicateReadFilter 2019-11-25T18:51:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829351-PrimaryLineReadFilter 2019-11-25T18:51:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829371-StrandOddsRatio 2019-11-25T18:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829391--Tool-Documentation-Index 2019-12-16T20:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829411-CheckFingerprint-Picard 2019-11-25T18:51:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829431-HasReadGroupReadFilter 2019-11-25T18:51:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829451-DetermineGermlineContigPloidy-BETA 2019-11-25T18:51:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829471-QualByDepth 2019-11-25T18:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829491-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T18:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829511-CountVariantsSpark-BETA 2019-11-25T18:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829531-IlluminaBasecallsToFastq-Picard 2019-11-25T18:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829551-SamFormatConverter-Picard 2019-11-25T18:51:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829571-ClusterCrosscheckMetrics-Picard 2019-11-25T18:51:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829591-ClipReads 2019-11-25T18:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829611-CollectSamErrorMetrics-Picard 2019-11-25T18:51:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829631-SoftClippedReadFilter 2019-11-25T18:51:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829651-DepthPerAlleleBySample 2019-11-25T18:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829671-CalculateReadGroupChecksum-Picard 2019-11-25T18:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829691-SetNmMdAndUqTags-Picard 2019-11-25T18:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829711-CompareMetrics-Picard 2019-11-25T18:55:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829731-FuncotateSegments-BETA 2019-11-25T18:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829751-CalculateFingerprintMetrics-Picard 2019-11-25T18:51:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829771-BwaSpark-BETA 2019-11-25T18:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829791-CollectAlignmentSummaryMetrics-Picard 2019-11-25T18:52:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829811-CollectSequencingArtifactMetrics-Picard 2019-11-25T18:52:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829831-MappedReadFilter 2019-11-25T18:52:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829851-GatherBQSRReports 2019-11-25T18:52:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829871-CalculateContamination 2019-11-25T18:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829891-PathSeqBuildKmers 2019-11-25T18:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829911-MakeSitesOnlyVcf-Picard 2019-11-25T18:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829931-CollectInsertSizeMetrics-Picard 2019-11-25T18:52:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829951-CollectReadCounts-BETA 2019-11-25T18:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829971-SortSamSpark-BETA 2019-11-25T18:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036829991-FilterIntervals 2019-11-25T18:52:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830011-MappingQualityRankSumTest 2019-11-25T18:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830031-MappingQualityNotZeroReadFilter 2019-11-25T18:52:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830051-HaplotypeCallerSpark-BETA 2019-11-25T18:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830071-SplitSamByNumberOfReads-Picard 2019-11-25T18:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830111-MateDifferentStrandReadFilter 2019-11-25T18:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830131-FilterMutectCalls 2019-11-25T18:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830151-SelectVariants 2019-11-25T18:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830171-IlluminaBasecallsToSam-Picard 2019-11-25T18:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830191-MappingQualityReadFilter 2019-11-25T18:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830211-PlatformUnitReadFilter 2019-11-25T18:52:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830231-HaplotypeCaller 2019-11-25T18:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830251-ReplaceSamHeader-Picard 2019-11-25T18:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830271-MateUnmappedAndUnmappedReadFilter 2019-11-25T18:52:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830291-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T18:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830311-SetNmAndUqTags-Picard 2019-11-25T18:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830331-MarkIlluminaAdapters-Picard 2019-11-25T18:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830351-SampleList 2019-11-25T18:52:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830371-MatchingBasesAndQualsReadFilter 2019-11-25T18:52:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830391-MeanQualityByCycleSpark-BETA 2019-11-25T18:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830411-CheckIlluminaDirectory-Picard 2019-11-25T18:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830431-LeftAlignAndTrimVariants 2019-11-25T18:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830451-ModelSegments-BETA 2019-11-25T18:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830471-RevertSamSpark-BETA 2019-11-25T18:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830491-ExtractIlluminaBarcodes-Picard 2019-11-25T18:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830511-AmbiguousBaseReadFilter 2019-11-25T18:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830531-BedToIntervalList-Picard 2019-11-25T18:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830551-RemoveNearbyIndels 2019-11-25T18:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830591-OriginalAlignment 2019-11-25T18:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830611-GoodCigarReadFilter 2019-11-25T18:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830631-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T18:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830651-PostprocessGermlineCNVCalls-BETA 2019-11-25T18:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830671-NotSupplementaryAlignmentReadFilter 2019-11-25T18:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830691-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T18:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830711-CollectWgsMetrics-Picard 2019-11-25T18:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830731-PairedReadFilter 2019-11-25T18:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830751-AS-ReadPosRankSumTest 2019-11-25T18:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830771-GetPileupSummaries-BETA 2019-11-25T18:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830791-FifoBuffer-Picard 2019-11-25T18:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830811-ExcessHet 2019-11-25T18:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830831-BaseRecalibrator 2019-11-25T18:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830851-RevertBaseQualityScores 2019-11-25T18:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830871-GatherTranches-BETA 2019-11-25T18:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830891-DownsampleSam-Picard 2019-11-25T18:56:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830911-ClippingRankSumTest 2019-11-25T18:53:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830931-CompareSAMs-Picard 2019-11-25T18:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830951-EstimateLibraryComplexityGATK-BETA 2019-11-25T18:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830971-PossibleDeNovo 2019-11-25T18:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036830991-DenoiseReadCounts-BETA 2019-11-25T18:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831111-GermlineCNVCaller-BETA 2019-11-25T18:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831131-UpdateVcfSequenceDictionary-Picard 2019-11-25T18:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831151-ReadNameReadFilter 2019-11-25T18:53:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831171-ScatterIntervalsByNs-Picard 2019-11-25T18:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831191-AS-InbreedingCoeff 2019-11-25T18:57:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831211-PlatformReadFilter 2019-11-25T18:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831231-BamIndexStats-Picard 2019-11-25T18:57:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831271-VcfFormatConverter-Picard 2019-11-25T18:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831291-AddOrReplaceReadGroups-Picard 2019-11-25T18:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831311-PlotModeledSegments-BETA 2019-11-25T18:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831331-CollectVariantCallingMetrics-Picard 2019-11-25T18:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831351-LiftoverVcf-Picard 2019-11-25T18:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831371-AddOATag-Picard 2019-11-25T18:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831391-Coverage 2019-11-25T18:57:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831411-ApplyBQSRSpark-BETA 2019-11-25T18:57:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831431-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T18:53:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831451-MergeVcfs-Picard 2019-11-25T18:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831471-CollectMultipleMetrics-Picard 2019-11-25T18:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831491-ExtractSVEvidenceSpark-BETA 2019-11-25T18:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831511-CollectAllelicCounts-BETA 2019-11-25T18:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831531-CNNScoreVariants-EXPERIMENTAL 2019-11-25T18:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831551-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T18:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831571-PreprocessIntervals-BETA 2019-11-25T18:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831591-FlagStat 2019-11-25T18:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831611-InbreedingCoeff 2019-11-25T18:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831631-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T18:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831651-FixMateInformation-Picard 2019-11-25T18:54:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831671-PrintVariantsSpark-BETA 2019-11-25T18:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831691-ValidateSamFile-Picard 2019-11-25T18:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831711-FastqToSam-Picard 2019-11-25T18:57:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831731-ReadGroupBlackListReadFilter 2019-11-25T18:54:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831751-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T18:54:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831771-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T18:54:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831791-CollectRnaSeqMetrics-Picard 2019-11-25T18:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831811-GatherVcfsCloud-BETA 2019-11-25T18:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831831-PathSeqScoreSpark 2019-11-25T18:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831851-RevertSam-Picard 2023-08-31T17:08:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831871-PassesVendorQualityCheckReadFilter 2019-11-25T18:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831891-AS-MappingQualityRankSumTest 2019-11-25T18:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831911-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T18:57:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831931-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T18:57:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831951-ReadPosRankSumTest 2019-11-25T18:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831971-BaseQuality 2019-11-25T18:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036831991-SeqIsStoredReadFilter 2019-11-25T18:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832011-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T18:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832031-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T18:57:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832051-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T18:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832071-SplitNCigarReads 2019-11-25T18:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832091-PileupSpark-BETA 2019-11-25T18:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832111-SplitVcfs-Picard 2019-11-25T18:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832131-FilterFuncotations-EXPERIMENTAL 2019-11-25T18:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832151-SplitSamByLibrary-Picard 2019-11-25T18:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832171-CrosscheckFingerprints-Picard 2019-11-25T18:57:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832191-GenotypeGVCFs 2019-11-25T18:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832211-FindBadGenomicKmersSpark-BETA 2019-11-25T18:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832231-Concordance-BETA 2019-11-25T18:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832251-BuildBamIndex-Picard 2019-11-25T18:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832271-CollectRrbsMetrics-Picard 2019-11-25T18:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832291-ReferenceBases 2019-11-25T18:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832311-MetricsReadFilter 2019-11-25T18:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832331-ValidAlignmentEndReadFilter 2019-11-25T18:58:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832351-QualityScoreDistributionSpark-BETA 2019-11-25T18:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832371-DepthPerSampleHC 2019-11-25T18:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832391-OrientationBiasReadCounts 2019-11-25T18:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832411-RenameSampleInVcf-Picard 2019-11-25T18:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832431-CreateReadCountPanelOfNormals-BETA 2019-11-25T18:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832471-CountBasesSpark-BETA 2019-11-25T18:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832491-ASEReadCounter 2019-11-25T18:58:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832511-FilterVariantTranches-EXPERIMENTAL 2019-11-25T18:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832531-CreateSomaticPanelOfNormals-BETA 2019-11-25T18:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832551-CheckPileup 2019-11-25T18:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832711-ChromosomeCounts 2019-11-25T19:01:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832731-NonChimericOriginalAlignmentReadFilter 2019-11-25T19:01:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832751-MeanQualityByCycle-Picard 2019-11-25T19:05:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832771-GenotypeConcordance-Picard 2019-11-25T19:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832791-Pileup 2019-11-25T19:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832811-RMSMappingQuality 2019-11-25T19:05:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832831-CollectQualityYieldMetrics-Picard 2019-11-25T19:01:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832851-PathSeqPipelineSpark 2019-11-25T19:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832871-CalcMetadataSpark-BETA 2019-11-25T19:06:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832891-AlignmentAgreesWithHeaderReadFilter 2019-11-25T19:01:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832931-AS-StrandOddsRatio 2019-11-25T19:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832951-FilterVcf-Picard 2019-11-25T19:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036832991-FixVcfHeader-Picard 2019-11-25T19:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833011-CollectHsMetrics-Picard 2019-11-25T19:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833031-GnarlyGenotyper-BETA 2019-11-25T19:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833051-ViewSam-Picard 2019-11-25T19:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833071-CountVariants 2019-11-25T19:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833091-NotDuplicateReadFilter 2019-11-25T19:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833111-VariantAnnotator-BETA 2019-11-25T19:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833131-FilterSamReads-Picard 2019-11-25T19:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833151-PrimaryLineReadFilter 2019-11-25T19:01:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833191-StrandOddsRatio 2019-11-25T19:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833211-CheckFingerprint-Picard 2019-11-25T19:01:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833231-HasReadGroupReadFilter 2019-11-25T19:01:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833251-DetermineGermlineContigPloidy-BETA 2019-11-25T19:01:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833271-UniqueAltReadCount 2019-11-25T19:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833291-NormalizeFasta-Picard 2019-11-25T19:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833311-UpdateVCFSequenceDictionary 2019-11-25T19:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833331-IlluminaBasecallsToFastq-Picard 2019-11-25T19:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833351-ClipReads 2019-11-25T19:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833371-CollectSamErrorMetrics-Picard 2019-11-25T19:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833391-SoftClippedReadFilter 2019-11-25T19:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833411-MarkDuplicatesSpark-BETA 2019-11-25T19:06:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833431-SetNmMdAndUqTags-Picard 2019-11-25T19:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833451-FuncotateSegments-BETA 2019-11-25T19:06:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833471-GatherBamFiles-Picard 2019-11-25T19:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833491-PathSeqBuildReferenceTaxonomy 2019-11-25T19:02:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833511-CollectAlignmentSummaryMetrics-Picard 2019-11-25T19:02:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833531-CollectSequencingArtifactMetrics-Picard 2019-11-25T19:02:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833551-GatherVcfs-Picard 2019-11-25T19:02:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833571-MappedReadFilter 2019-11-25T19:02:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833591-MarkDuplicatesWithMateCigar-Picard 2019-11-25T19:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833611-ApplyBQSR 2019-11-25T19:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833631-CpxVariantReInterpreterSpark-BETA 2019-11-25T19:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833651-PathSeqBuildKmers 2019-11-25T19:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833671-MakeSitesOnlyVcf-Picard 2019-11-25T19:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833691-CollectReadCounts-BETA 2019-11-25T19:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833711-SortSamSpark-BETA 2019-11-25T19:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833731-LeftAlignIndels 2019-11-25T19:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833751-MappingQualityRankSumTest 2019-11-25T19:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833771-SplitSamByNumberOfReads-Picard 2019-11-25T19:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833791-MateDifferentStrandReadFilter 2019-11-25T19:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833811-NonNFastaSize-Picard 2019-11-25T19:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833831-FilterMutectCalls 2019-11-25T19:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833851-CalculateMixingFractions 2019-11-25T19:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833871-SelectVariants 2019-11-25T19:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833891-AccumulateVariantCallingMetrics-Picard 2019-11-25T19:02:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833911-IlluminaBasecallsToSam-Picard 2019-11-25T19:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833931-ReadGroupReadFilter 2019-11-25T19:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833951-MappingQualityReadFilter 2019-11-25T19:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036833991-CollectQualityYieldMetricsSpark-BETA 2019-11-25T19:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834011-PlatformUnitReadFilter 2019-11-25T19:03:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834031-OxoGReadCounts 2019-11-25T19:03:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834051-CreateHadoopBamSplittingIndex-BETA 2019-11-25T19:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834071-PrintReads 2019-11-25T19:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834091-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T19:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834111-CrosscheckReadGroupFingerprints-Picard 2019-11-25T19:03:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834131-HaplotypeCaller 2019-11-25T19:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834151-ValidAlignmentStartReadFilter 2019-11-25T19:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834171-ReadsPipelineSpark-BETA 2019-11-25T19:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834191-CollectIlluminaLaneMetrics-Picard 2019-11-25T19:07:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834211-CountBasesInReference 2019-11-25T19:07:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834231-PolymorphicNuMT 2019-11-25T19:03:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834251-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T19:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834271-PathSeqBwaSpark 2019-11-25T19:07:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834291-MarkIlluminaAdapters-Picard 2019-11-25T19:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834311-SampleList 2019-11-25T19:03:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834331-MatchingBasesAndQualsReadFilter 2019-11-25T19:03:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834351-CheckIlluminaDirectory-Picard 2019-11-25T19:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834371-CollectBaseDistributionByCycle-Picard 2019-11-25T19:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834391-ReblockGVCF-EXPERIMENTAL 2019-11-25T19:07:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834411-MergeBamAlignment-Picard 2019-11-25T19:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834431-FixMisencodedBaseQualityReads 2019-11-25T19:07:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834451-ModelSegments-BETA 2019-11-25T19:03:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834471-RevertSamSpark-BETA 2019-11-25T19:07:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834491-ExtractIlluminaBarcodes-Picard 2019-11-25T19:07:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834511-AmbiguousBaseReadFilter 2019-11-25T19:03:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834531-BedToIntervalList-Picard 2019-11-25T19:07:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834551-CompareDuplicatesSpark-BETA 2019-11-25T19:07:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834571-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T19:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834591-OriginalAlignment 2019-11-25T19:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834611-MarkDuplicates-Picard 2019-11-25T19:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834631-CreateSequenceDictionary-Picard 2019-11-25T19:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834651-VcfToAdpc-Picard 2019-11-25T19:03:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834671-GoodCigarReadFilter 2019-11-25T19:03:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834691-PositionBasedDownsampleSam-Picard 2019-11-25T19:03:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834711-ReorderSam-Picard 2019-11-25T19:03:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834731-GenotypeSummaries 2019-11-25T19:03:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834751-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T19:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834771-CollectWgsMetrics-Picard 2019-11-25T19:07:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834791-PairedReadFilter 2019-11-25T19:03:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834811-AS-ReadPosRankSumTest 2019-11-25T19:07:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834831-GetPileupSummaries-BETA 2019-11-25T19:07:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834851-ExcessHet 2019-11-25T19:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834871-VariantFiltration 2019-11-25T19:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834891-LikelihoodRankSumTest 2019-11-25T19:03:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834911-RevertBaseQualityScores 2019-11-25T19:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834931-GatherTranches-BETA 2019-11-25T19:04:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834951-ClippingRankSumTest 2019-11-25T19:04:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834971-CompareSAMs-Picard 2019-11-25T19:07:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036834991-BQSRPipelineSpark-BETA 2019-11-25T19:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835011-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2019-11-25T19:07:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835031-PossibleDeNovo 2019-11-25T19:04:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835051-BaseQualityRankSumTest 2019-11-25T19:04:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835071-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T19:07:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835091-ApplyVQSR 2019-11-25T19:07:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835111-MappingQualityZero 2019-11-25T19:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835131-AS-InbreedingCoeff 2019-11-25T19:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835151-BamIndexStats-Picard 2019-11-25T19:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835171-FilterMutectCalls 2019-11-25T19:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835191-AddOrReplaceReadGroups-Picard 2019-11-25T19:04:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835211-CollectVariantCallingMetrics-Picard 2019-11-25T19:04:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835231-CombineGVCFs 2019-11-25T19:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835251-CollectGcBiasMetrics-Picard 2019-11-25T19:04:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835271-LiftoverVcf-Picard 2019-11-25T19:07:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835291-AddOATag-Picard 2019-11-25T19:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835311-ReadPosition 2019-11-25T19:04:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835331-CollectMultipleMetrics-Picard 2019-11-25T19:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835351-ValidateVariants 2019-11-25T19:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835371-CollectAllelicCounts-BETA 2019-11-25T19:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835391-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T19:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835411-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T19:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835431-PreprocessIntervals-BETA 2019-11-25T19:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835451-QualityScoreDistribution-Picard 2019-11-25T19:04:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835471-InbreedingCoeff 2019-11-25T19:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835491-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T19:08:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835511-PrintVariantsSpark-BETA 2019-11-25T19:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835531-FastqToSam-Picard 2019-11-25T19:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835551-SamToFastq-Picard 2019-11-25T19:08:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835571-SortSam-Picard 2019-11-25T19:08:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835591-MergeSamFiles-Picard 2019-11-25T19:08:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835611-GatherVcfsCloud-BETA 2019-11-25T19:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835631-AnnotateIntervals-BETA 2019-11-25T19:08:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835651-PathSeqScoreSpark 2019-11-25T19:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835671-PassesVendorQualityCheckReadFilter 2019-11-25T19:04:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835691-SplitReads 2019-11-25T19:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835711-AS-MappingQualityRankSumTest 2019-11-25T19:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835731-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T19:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835751-BaseQuality 2019-11-25T19:05:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835771-SeqIsStoredReadFilter 2019-11-25T19:05:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835791-VariantRecalibrator 2019-11-25T19:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835811-PathSeqFilterSpark 2019-11-25T19:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835831-PlotDenoisedCopyRatios-BETA 2019-11-25T19:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835851-FastaAlternateReferenceMaker 2019-11-25T19:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835871-UnmarkDuplicates 2019-11-25T19:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835891-ProperlyPairedReadFilter 2019-11-25T19:05:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835911-CigarContainsNoNOperator 2019-11-25T19:05:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835931-SplitVcfs-Picard 2019-11-25T19:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835971-SplitSamByLibrary-Picard 2019-11-25T19:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036835991-CrosscheckFingerprints-Picard 2019-11-25T19:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836011-AnalyzeSaturationMutagenesis-BETA 2019-11-25T19:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836031-BuildBamIndex-Picard 2019-11-25T19:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836051-NotSecondaryAlignmentReadFilter 2019-11-25T19:05:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836071-FindMendelianViolations-Picard 2019-11-25T19:08:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836091-ReferenceBases 2019-11-25T19:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836111-IndexFeatureFile 2019-11-25T19:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836131-AlleleFraction 2019-11-25T19:08:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836151-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T19:05:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836171-CountNs 2019-11-25T19:05:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836191-RenameSampleInVcf-Picard 2019-11-25T19:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836211-CountReadsSpark-BETA 2019-11-25T19:08:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836231-CountBasesSpark-BETA 2019-11-25T19:08:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836251-PrintReadsSpark-BETA 2019-11-25T19:08:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836271-ASEReadCounter 2019-11-25T19:08:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836291-CheckPileup 2019-11-25T19:08:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836311-GtcToVcf-Picard 2019-11-25T19:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836331-CheckTerminatorBlock-Picard 2019-11-25T19:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836511-CollectIndependentReplicateMetrics-Picard-BETA 2019-11-25T19:11:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836531-ChromosomeCounts 2019-11-25T19:11:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836551-NonChimericOriginalAlignmentReadFilter 2019-11-25T19:11:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836571-MeanQualityByCycle-Picard 2019-11-25T19:16:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836591-GenotypeConcordance-Picard 2019-11-25T19:16:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836611-Pileup 2019-11-25T19:16:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836631-WellformedReadFilter 2019-11-25T19:16:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836651-SampleReadFilter 2019-11-25T19:12:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836671-RMSMappingQuality 2019-11-25T19:16:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836691-CalcMetadataSpark-BETA 2019-11-25T19:16:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836711-SecondOfPairReadFilter 2019-11-25T19:12:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836731-AlignmentAgreesWithHeaderReadFilter 2019-11-25T19:12:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836751-FilterVcf-Picard 2019-11-25T19:12:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836771-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T19:16:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836791-VariantEval-BETA 2019-11-25T19:16:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836811-FixVcfHeader-Picard 2019-11-25T19:16:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836831-CollectHsMetrics-Picard 2019-11-25T19:16:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836851-EstimateLibraryComplexity-Picard 2019-11-25T19:16:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836871-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T19:16:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836891-CountVariants 2019-11-25T19:16:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836911-AllowAllReadsReadFilter 2019-11-25T19:12:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836931-NotDuplicateReadFilter 2019-11-25T19:12:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836951-FilterSamReads-Picard 2019-11-25T19:16:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836971-CountBases 2019-11-25T19:16:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036836991-StrandOddsRatio 2019-11-25T19:16:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837011--Tool-Documentation-Index 2019-12-16T20:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837031-CheckFingerprint-Picard 2019-11-25T19:12:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837051-HasReadGroupReadFilter 2019-11-25T19:12:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837071-FindBreakpointEvidenceSpark-BETA 2019-11-25T19:16:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837091-QualByDepth 2019-11-25T19:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837111-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T19:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837131-CountVariantsSpark-BETA 2019-11-25T19:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837171-SamFormatConverter-Picard 2019-11-25T19:12:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837191-FisherStrand 2019-11-25T19:16:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837211-ClipReads 2019-11-25T19:16:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837231-CollectSamErrorMetrics-Picard 2019-11-25T19:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837251-SoftClippedReadFilter 2019-11-25T19:12:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837271-GetSampleName-BETA 2019-11-25T19:16:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837291-DepthPerAlleleBySample 2019-11-25T19:16:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837311-CalculateReadGroupChecksum-Picard 2019-11-25T19:16:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837331-CompareMetrics-Picard 2019-11-25T19:16:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837351-GatherBamFiles-Picard 2019-11-25T19:12:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837371-CalculateFingerprintMetrics-Picard 2019-11-25T19:12:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837391-AnnotateVcfWithBamDepth 2019-11-25T19:16:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837411-GatherVcfs-Picard 2019-11-25T19:12:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837431-MappedReadFilter 2019-11-25T19:12:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837451-CpxVariantReInterpreterSpark-BETA 2019-11-25T19:16:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837471-PathSeqBuildKmers 2019-11-25T19:16:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837491-CollectInsertSizeMetrics-Picard 2019-11-25T19:13:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837511-StrandBiasBySample 2019-11-25T19:16:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837531-CollectReadCounts-BETA 2019-11-25T19:16:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837551-SortSamSpark-BETA 2019-11-25T19:16:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837571-LeftAlignIndels 2019-11-25T19:16:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837591-MappingQualityNotZeroReadFilter 2019-11-25T19:13:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837611-SplitSamByNumberOfReads-Picard 2019-11-25T19:17:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837631-MateDifferentStrandReadFilter 2019-11-25T19:17:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837651-NonNFastaSize-Picard 2019-11-25T19:17:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837671-SelectVariants 2019-11-25T19:17:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837691-AccumulateVariantCallingMetrics-Picard 2019-11-25T19:13:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837711-ReadGroupReadFilter 2019-11-25T19:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837731-CollectQualityYieldMetricsSpark-BETA 2019-11-25T19:17:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837751-PlatformUnitReadFilter 2019-11-25T19:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837771-OxoGReadCounts 2019-11-25T19:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837791-CreateHadoopBamSplittingIndex-BETA 2019-11-25T19:17:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837811-PrintReads 2019-11-25T19:17:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837831-CrosscheckReadGroupFingerprints-Picard 2019-11-25T19:13:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837871-ValidAlignmentStartReadFilter 2019-11-25T19:17:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837891-CountBasesInReference 2019-11-25T19:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837911-PolymorphicNuMT 2019-11-25T19:13:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837931-VcfToIntervalList-Picard 2019-11-25T19:17:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837951-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T19:13:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837971-PathSeqBwaSpark 2019-11-25T19:17:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036837991-MarkIlluminaAdapters-Picard 2020-10-12T13:00:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838011-SampleList 2019-11-25T19:13:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838031-MatchingBasesAndQualsReadFilter 2019-11-25T19:13:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838051-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T19:17:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838071-FragmentLength 2019-11-25T19:13:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838091-CollectBaseDistributionByCycle-Picard 2019-11-25T19:13:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838131-FixMisencodedBaseQualityReads 2019-11-25T19:17:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838171-ModelSegments-BETA 2019-11-25T19:13:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838191-ExtractIlluminaBarcodes-Picard 2019-11-25T19:17:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838211-RemoveNearbyIndels 2019-11-25T19:17:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838231-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T19:17:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838251-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T19:17:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838271-OriginalAlignment 2019-11-25T19:14:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838291-CreateSequenceDictionary-Picard 2019-11-25T19:17:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838311-VcfToAdpc-Picard 2019-11-25T19:14:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838331-ReorderSam-Picard 2019-11-25T19:14:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838351-PostprocessGermlineCNVCalls-BETA 2019-11-25T19:17:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838371-NotSupplementaryAlignmentReadFilter 2019-11-25T19:14:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838391-PairedReadFilter 2019-11-25T19:14:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838411-ExcessHet 2019-11-25T19:14:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838431-VariantFiltration 2019-11-25T19:17:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838451-BaseRecalibrator 2019-11-25T19:17:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838471-GatherTranches-BETA 2019-11-25T19:14:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838491-BQSRPipelineSpark-BETA 2019-11-25T19:17:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838511-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2019-11-25T19:17:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838531-PossibleDeNovo 2019-11-25T19:14:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838551-ApplyVQSR 2019-11-25T19:17:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838571-UpdateVcfSequenceDictionary-Picard 2019-11-25T19:14:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838591-CallCopyRatioSegments-BETA 2019-11-25T19:14:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838611-ScatterIntervalsByNs-Picard 2019-11-25T19:17:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838631-AS-InbreedingCoeff 2019-11-25T19:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838651-BamIndexStats-Picard 2019-11-25T19:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838671-Mutect2 2019-11-25T19:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838691-VcfFormatConverter-Picard 2019-11-25T19:17:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838711-AddOrReplaceReadGroups-Picard 2019-11-25T19:14:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838731-PlotModeledSegments-BETA 2019-11-25T19:14:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838751-CollectGcBiasMetrics-Picard 2019-11-25T19:14:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838771-LiftoverVcf-Picard 2019-11-25T19:17:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838791-ReadPosition 2019-11-25T19:14:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838811-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T19:18:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838831-CollectMultipleMetrics-Picard 2019-11-25T19:18:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838851-CNNScoreVariants-EXPERIMENTAL 2019-11-25T19:18:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838871-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T19:14:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838891-PreprocessIntervals-BETA 2019-11-25T19:18:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838911-QualityScoreDistribution-Picard 2019-11-25T19:14:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838931-FlagStat 2019-11-25T19:18:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838951-BaitDesigner-Picard 2019-11-25T19:18:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838971-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T19:18:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036838991-PrintVariantsSpark-BETA 2019-11-25T19:18:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839011-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T19:15:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839031-FuncotatorDataSourceDownloader-BETA 2019-11-25T19:15:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839051-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T19:15:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839071-GatherVcfsCloud-BETA 2019-11-25T19:18:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839091-AnnotateIntervals-BETA 2019-11-25T19:18:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839111-PathSeqScoreSpark 2019-11-25T19:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839131-PassesVendorQualityCheckReadFilter 2019-11-25T19:15:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839151-SplitReads 2019-11-25T19:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839171-AS-MappingQualityRankSumTest 2019-11-25T19:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839191-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T19:18:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839211-ReadPosRankSumTest 2019-11-25T19:15:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839231-BaseQuality 2019-11-25T19:15:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839251-VariantRecalibrator 2019-11-25T19:18:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839271-PathSeqFilterSpark 2019-11-25T19:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839291-FastaAlternateReferenceMaker 2019-11-25T19:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839311-UnmarkDuplicates 2019-11-25T19:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839331-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T19:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839351-NonZeroFragmentLengthReadFilter 2019-11-25T19:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839371-PileupSpark-BETA 2019-11-25T19:18:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839391-SplitVcfs-Picard 2019-11-25T19:18:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839431-CrosscheckFingerprints-Picard 2019-11-25T19:18:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839451-CNNVariantTrain-EXPERIMENTAL 2019-11-25T19:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839471-TandemRepeat 2019-11-25T19:15:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839491-FindBadGenomicKmersSpark-BETA 2019-11-25T19:18:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839511-AddCommentsToBam-Picard 2019-11-25T19:18:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839531-AnalyzeSaturationMutagenesis-BETA 2019-11-25T19:18:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839551-AS-QualByDepth 2019-11-25T19:18:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839571-FragmentLengthReadFilter 2019-11-25T19:15:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839591-BuildBamIndex-Picard 2019-11-25T19:18:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839611-CollectRrbsMetrics-Picard 2019-11-25T19:15:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839631-ReferenceBases 2019-11-25T19:15:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839651-MetricsReadFilter 2019-11-25T19:15:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839671-ValidAlignmentEndReadFilter 2019-11-25T19:18:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839691-FastaReferenceMaker 2019-11-25T19:18:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839711-QualityScoreDistributionSpark-BETA 2019-11-25T19:18:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839731-DepthPerSampleHC 2019-11-25T19:18:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839751-AlleleFraction 2019-11-25T19:18:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839771-OrientationBiasReadCounts 2019-11-25T19:15:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839791-MappingQualityAvailableReadFilter 2019-11-25T19:15:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839811-CreateReadCountPanelOfNormals-BETA 2019-11-25T19:15:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839831-CountReadsSpark-BETA 2019-11-25T19:18:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839851-CountBasesSpark-BETA 2019-11-25T19:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839871-CheckPileup 2019-11-25T19:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036839891-ReadLengthReadFilter 2019-11-25T19:16:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851731-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T20:04:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851751-LibraryReadFilter 2019-11-25T20:04:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851771-NonChimericOriginalAlignmentReadFilter 2019-11-25T20:04:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851791-MeanQualityByCycle-Picard 2019-11-25T20:09:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851811-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T20:09:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851831-GenotypeConcordance-Picard 2019-11-25T20:09:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851851-Pileup 2019-11-25T20:09:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851871-SampleReadFilter 2019-11-25T20:05:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851891-AnalyzeCovariates 2019-11-25T20:09:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851911-RMSMappingQuality 2019-11-25T20:09:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851931-Funcotator-BETA 2019-11-25T20:09:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851951-PathSeqPipelineSpark 2019-11-25T20:09:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036851991-AlignmentAgreesWithHeaderReadFilter 2019-11-25T20:05:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852011-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T20:09:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852031-AnnotatePairOrientation-BETA 2019-11-25T20:09:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852051-VariantEval-BETA 2019-11-25T20:09:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852071-CountReads 2019-11-25T20:09:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852091-EstimateLibraryComplexity-Picard 2019-11-25T20:09:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852111-ViewSam-Picard 2019-11-25T20:09:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852131-CountVariants 2019-11-25T20:09:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852151-LiftOverIntervalList-Picard 2019-11-25T20:05:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852171-NotDuplicateReadFilter 2019-11-25T20:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852191-PrimaryLineReadFilter 2019-11-25T20:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852211-CollectMultipleMetricsSpark-BETA 2019-11-25T20:09:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852231-CountBases 2019-11-25T20:09:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852251-HasReadGroupReadFilter 2019-11-25T20:05:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852271-MappingQuality 2019-11-25T20:05:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852291-VariantsToTable 2019-11-25T20:09:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852331-CountVariantsSpark-BETA 2019-11-25T20:09:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852351-IlluminaBasecallsToFastq-Picard 2019-11-25T20:09:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852371-SamFormatConverter-Picard 2019-11-25T20:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852391-FisherStrand 2019-11-25T20:09:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852431-ClusterCrosscheckMetrics-Picard 2019-11-25T20:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852471-MarkDuplicatesSpark-BETA 2019-11-25T20:09:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852491-DepthPerAlleleBySample 2019-11-25T20:09:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852511-CalculateReadGroupChecksum-Picard 2019-11-25T20:09:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852531-CompareMetrics-Picard 2019-11-25T20:09:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852551-FuncotateSegments-BETA 2019-11-25T20:09:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852571-GatherBamFiles-Picard 2019-11-25T20:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852591-PathSeqBuildReferenceTaxonomy 2019-11-25T20:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852611-AS-FisherStrand 2019-11-25T20:10:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852631-BwaSpark-BETA 2019-11-25T20:10:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852651-CollectAlignmentSummaryMetrics-Picard 2019-11-25T20:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852671-AnnotateVcfWithBamDepth 2019-11-25T20:10:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852691-CollectSequencingArtifactMetrics-Picard 2019-11-25T20:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852711-MappedReadFilter 2019-11-25T20:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852731-ExtractSequences-Picard 2019-11-25T20:10:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852751-GatherBQSRReports 2019-11-25T20:06:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852771-ApplyBQSR 2019-11-25T20:10:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852791-MakeSitesOnlyVcf-Picard 2019-11-25T20:10:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852811-IntervalListTools-Picard 2019-11-25T20:10:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852871-StrandBiasBySample 2019-11-25T20:10:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852891-CollectReadCounts-BETA 2019-11-25T20:10:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852911-SortSamSpark-BETA 2019-11-25T20:10:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852931-LeftAlignIndels 2019-11-25T20:10:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852951-FilterIntervals-BETA 2019-11-25T20:06:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852971-MappingQualityRankSumTest 2019-11-25T20:10:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036852991-MappingQualityNotZeroReadFilter 2019-11-25T20:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853011-HaplotypeCallerSpark-BETA 2019-11-25T20:10:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853031-CollectJumpingLibraryMetrics-Picard 2019-11-25T20:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853051-SplitSamByNumberOfReads-Picard 2019-11-25T20:10:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853071-MateDifferentStrandReadFilter 2019-11-25T20:10:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853091-NonNFastaSize-Picard 2019-11-25T20:10:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853151-CalculateMixingFractions 2019-11-25T20:10:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853171-AccumulateVariantCallingMetrics-Picard 2019-11-25T20:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853191-IlluminaBasecallsToSam-Picard 2019-11-25T20:10:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853211-MappingQualityReadFilter 2019-11-25T20:10:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853231-CollectQualityYieldMetricsSpark-BETA 2019-11-25T20:10:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853251-PlatformUnitReadFilter 2019-11-25T20:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853271-OxoGReadCounts 2019-11-25T20:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853291-PrintReads 2019-11-25T20:10:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853311-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-11-25T20:10:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853331-HaplotypeCaller 2019-11-25T20:10:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853351-ValidAlignmentStartReadFilter 2019-11-25T20:10:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853371-ReadsPipelineSpark-BETA 2019-11-25T20:10:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853391-ReplaceSamHeader-Picard 2019-11-25T20:10:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853431-CountBasesInReference 2019-11-25T20:10:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853451-PolymorphicNuMT 2019-11-25T20:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853471-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T20:10:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853491-MarkIlluminaAdapters-Picard 2019-11-25T20:10:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853511-SampleList 2019-11-25T20:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853531-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T20:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853551-MeanQualityByCycleSpark-BETA 2019-11-25T20:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853571-FragmentLength 2019-11-25T20:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853591-CheckIlluminaDirectory-Picard 2019-11-25T20:10:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853611-CollectTargetedPcrMetrics-Picard 2019-11-25T20:10:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853631-CollectBaseDistributionByCycle-Picard 2019-11-25T20:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853651-MergeBamAlignment-Picard 2019-11-25T20:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853671-FixMisencodedBaseQualityReads 2019-11-25T20:10:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853691-LeftAlignAndTrimVariants 2019-11-25T20:10:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853731-AmbiguousBaseReadFilter 2019-11-25T20:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853751-RemoveNearbyIndels 2019-11-25T20:10:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853771-CompareDuplicatesSpark-BETA 2019-11-25T20:10:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853791-CollectRawWgsMetrics-Picard 2019-11-25T20:10:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853811-MarkDuplicates-Picard 2019-11-25T20:10:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853831-CreateSequenceDictionary-Picard 2019-11-25T20:10:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853851-VcfToAdpc-Picard 2019-11-25T20:07:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853871-GoodCigarReadFilter 2019-11-25T20:07:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853891-PositionBasedDownsampleSam-Picard 2019-11-25T20:07:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853911-ReorderSam-Picard 2019-11-25T20:07:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853931-PostprocessGermlineCNVCalls-BETA 2019-11-25T20:10:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853951-CollectWgsMetrics-Picard 2019-11-25T20:10:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853971-PairedReadFilter 2019-11-25T20:07:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036853991-LikelihoodRankSumTest 2019-11-25T20:07:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854011-BaseRecalibrator 2019-11-25T20:10:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854031-RevertBaseQualityScores 2019-11-25T20:10:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854051-GatherTranches-BETA 2019-11-25T20:07:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854071-DownsampleSam-Picard 2019-11-25T20:11:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854091-CompareSAMs-Picard 2019-11-25T20:11:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854111-BQSRPipelineSpark-BETA 2019-11-25T20:11:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854131-EstimateLibraryComplexityGATK-BETA 2019-11-25T20:11:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854151-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T20:11:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854171-PossibleDeNovo 2019-11-25T20:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854191-CollectInsertSizeMetricsSpark-BETA 2019-11-25T20:11:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854211-DenoiseReadCounts-BETA 2019-11-25T20:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854231-UpdateVcfSequenceDictionary-Picard 2019-11-25T20:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854251-ReadNameReadFilter 2019-11-25T20:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854271-MappingQualityZero 2019-11-25T20:11:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854291-CallCopyRatioSegments-BETA 2019-11-25T20:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854311-ScatterIntervalsByNs-Picard 2019-11-25T20:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854331-PlatformReadFilter 2019-11-25T20:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854351-BamIndexStats-Picard 2019-11-25T20:11:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854371-Mutect2 2019-11-25T20:11:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854391-VcfFormatConverter-Picard 2019-11-25T20:11:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854411-AddOrReplaceReadGroups-Picard 2019-11-25T20:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854431-PlotModeledSegments-BETA 2019-11-25T20:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854451-LiftoverVcf-Picard 2019-11-25T20:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854471-AddOATag-Picard 2019-11-25T20:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854491-ReadPosition 2019-11-25T20:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854511-Coverage 2019-11-25T20:11:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854531-ReadStrandFilter 2019-11-25T20:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854551-ApplyBQSRSpark-BETA 2019-11-25T20:11:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854571-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T20:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854591-CollectAllelicCounts-BETA 2019-11-25T20:11:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854611-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T20:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854631-PreprocessIntervals-BETA 2019-11-25T20:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854651-FlagStat 2019-11-25T20:11:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854671-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T20:11:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854691-FixMateInformation-Picard 2019-11-25T20:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854711-PrintVariantsSpark-BETA 2019-11-25T20:11:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854731-ValidateSamFile-Picard 2024-09-15T13:59:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854751-FastqToSam-Picard 2019-11-25T20:11:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854771-ReadGroupBlackListReadFilter 2019-11-25T20:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854791-SortSam-Picard 2019-11-25T20:11:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854811-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T20:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854831-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-11-25T20:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854851-MergeSamFiles-Picard 2019-11-25T20:11:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854871-GatherVcfsCloud-BETA 2019-11-25T20:11:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854891-PathSeqScoreSpark 2019-11-25T20:11:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854911-PassesVendorQualityCheckReadFilter 2019-11-25T20:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854931-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T20:11:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854951-SeqIsStoredReadFilter 2019-11-25T20:08:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854971-IntervalOverlapReadFilter 2019-11-25T20:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036854991-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T20:11:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855011-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T20:11:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855031-SplitNCigarReads 2019-11-25T20:11:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855051-PileupSpark-BETA 2019-11-25T20:11:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855071-ProperlyPairedReadFilter 2019-11-25T20:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855091-FilterFuncotations-EXPERIMENTAL 2019-11-25T20:11:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855111-SplitSamByLibrary-Picard 2019-11-25T20:11:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855131-GenotypeGVCFs 2019-11-25T20:12:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855151-FindBadGenomicKmersSpark-BETA 2019-11-25T20:12:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855171-AddCommentsToBam-Picard 2019-11-25T20:12:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855191-AnalyzeSaturationMutagenesis-BETA 2019-11-25T20:12:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855211-Concordance-BETA 2019-11-25T20:12:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855231-FragmentLengthReadFilter 2019-11-25T20:08:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855251-CollectRrbsMetrics-Picard 2019-11-25T20:08:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855271-FindMendelianViolations-Picard 2019-11-25T20:12:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855291-ReferenceBases 2019-11-25T20:08:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855311-IndexFeatureFile 2019-11-25T20:08:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855331-ValidAlignmentEndReadFilter 2019-11-25T20:12:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855351-FastaReferenceMaker 2019-11-25T20:12:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855371-QualityScoreDistributionSpark-BETA 2019-11-25T20:12:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855391-DepthPerSampleHC 2019-11-25T20:12:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855431-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T20:09:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855451-RenameSampleInVcf-Picard 2019-11-25T20:12:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855471-CreateReadCountPanelOfNormals-BETA 2019-11-25T20:09:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855491-CountReadsSpark-BETA 2019-11-25T20:12:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855511-CountBasesSpark-BETA 2019-11-25T20:12:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855531-CheckPileup 2019-11-25T20:12:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855551-CheckTerminatorBlock-Picard 2019-11-25T20:09:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855791-ChromosomeCounts 2019-11-25T20:16:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855811-LibraryReadFilter 2019-11-25T20:16:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855831-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-11-25T20:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855851-MeanQualityByCycle-Picard 2019-11-25T20:20:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855871-OverclippedReadFilter 2019-11-25T20:16:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855891-WellformedReadFilter 2019-11-25T20:20:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855911-RMSMappingQuality 2019-11-25T20:20:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855931-FirstOfPairReadFilter 2019-11-25T20:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855951-Funcotator-BETA 2019-11-25T20:20:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855971-CalcMetadataSpark-BETA 2019-11-25T20:20:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036855991-SecondOfPairReadFilter 2019-11-25T20:16:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856011-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-11-25T20:20:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856031-VariantEval-BETA 2019-11-25T20:20:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard 2019-11-25T20:20:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856071-ViewSam-Picard 2019-11-25T20:21:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856091-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T20:21:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856131-BamToBfq-Picard 2019-11-25T20:16:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856151-FilterSamReads-Picard 2019-11-25T20:21:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856171-CountBases 2019-11-25T20:21:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856191-StrandOddsRatio 2019-11-25T20:21:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856231--Tool-Documentation-Index 2019-12-16T20:19:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856251-CheckFingerprint-Picard 2019-11-25T20:17:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856271-HasReadGroupReadFilter 2019-11-25T20:17:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856291-DetermineGermlineContigPloidy-BETA 2019-11-25T20:17:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856311-FindBreakpointEvidenceSpark-BETA 2019-11-25T20:21:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856331-UniqueAltReadCount 2019-11-25T20:17:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856351-QualByDepth 2019-11-25T20:21:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856371-CountVariantsSpark-BETA 2019-11-25T20:21:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856391-IlluminaBasecallsToFastq-Picard 2019-11-25T20:21:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856411-SamFormatConverter-Picard 2019-11-25T20:17:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856451-ClusterCrosscheckMetrics-Picard 2019-11-25T20:17:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856471-CollectSamErrorMetrics-Picard 2019-11-25T20:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856491-SoftClippedReadFilter 2019-11-25T20:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856511-MarkDuplicatesSpark-BETA 2019-11-25T20:21:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856531-CalculateReadGroupChecksum-Picard 2019-11-25T20:21:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856551-CompareMetrics-Picard 2019-11-25T20:21:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856571-GatherBamFiles-Picard 2019-11-25T20:17:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856591-CompareBaseQualities 2019-11-25T20:17:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856611-BwaSpark-BETA 2019-11-25T20:21:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856631-MappedReadFilter 2019-11-25T20:17:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856651-ExtractSequences-Picard 2019-11-25T20:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856671-ApplyBQSR 2019-11-25T20:21:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856691-CpxVariantReInterpreterSpark-BETA 2019-11-25T20:21:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856711-MakeSitesOnlyVcf-Picard 2019-11-25T20:21:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856731-CollectInsertSizeMetrics-Picard 2019-11-25T20:17:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856751-CollectReadCounts-BETA 2019-11-25T20:21:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856771-FilterIntervals-BETA 2019-11-25T20:17:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856791-MateDifferentStrandReadFilter 2019-11-25T20:21:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856811-NonNFastaSize-Picard 2019-11-25T20:21:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856831-FilterMutectCalls 2021-04-12T12:47:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856851-BaseRecalibratorSpark-BETA 2019-11-25T20:21:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856871-CalculateMixingFractions 2019-11-25T20:21:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856891-SelectVariants 2019-11-25T20:21:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856911-ReadGroupReadFilter 2019-11-25T20:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856931-GenomicsDBImport 2020-08-01T00:23:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856951-CollectQualityYieldMetricsSpark-BETA 2019-11-25T20:21:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856971-PlatformUnitReadFilter 2019-11-25T20:17:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036856991-OxoGReadCounts 2019-11-25T20:17:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857011-CrosscheckReadGroupFingerprints-Picard 2019-11-25T20:17:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857031-ReadsPipelineSpark-BETA 2019-11-25T20:21:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857051-ReplaceSamHeader-Picard 2019-11-25T20:21:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857071-MateUnmappedAndUnmappedReadFilter 2019-11-25T20:18:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857091-CollectIlluminaLaneMetrics-Picard 2019-11-25T20:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857111-CountBasesInReference 2019-11-25T20:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857131-VcfToIntervalList-Picard 2019-11-25T20:21:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857151-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T20:21:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857171-PathSeqBwaSpark 2019-11-25T20:21:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857191-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T20:22:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857211-MeanQualityByCycleSpark-BETA 2019-11-25T20:22:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857231-FragmentLength 2019-11-25T20:18:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857251-CollectTargetedPcrMetrics-Picard 2019-11-25T20:22:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857271-LeftAlignAndTrimVariants 2019-11-25T20:22:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857311-ModelSegments-BETA 2019-11-25T20:18:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857331-ExtractIlluminaBarcodes-Picard 2019-11-25T20:22:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857351-AmbiguousBaseReadFilter 2019-11-25T20:18:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857371-BedToIntervalList-Picard 2019-11-25T20:22:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857391-FilterByOrientationBias-EXPERIMENTAL 2019-11-25T20:22:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857411-GoodCigarReadFilter 2019-11-25T20:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857431-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T20:18:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857451-PostprocessGermlineCNVCalls-BETA 2019-11-25T20:22:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857471-NotSupplementaryAlignmentReadFilter 2019-11-25T20:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857491-GenotypeSummaries 2019-11-25T20:18:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857511-FlagStatSpark-BETA 2019-11-25T20:22:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857531-CollectWgsMetrics-Picard 2019-11-25T20:22:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857551-PairedReadFilter 2019-11-25T20:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857571-ExcessHet 2019-11-25T20:18:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857591-LikelihoodRankSumTest 2019-11-25T20:18:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857611-RevertBaseQualityScores 2019-11-25T20:22:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857631-GatherTranches-BETA 2019-11-25T20:18:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857651-DownsampleSam-Picard 2019-11-25T20:22:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857671-ClippingRankSumTest 2019-11-25T20:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857691-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-11-25T20:22:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857711-PossibleDeNovo 2019-11-25T20:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857731-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-11-25T20:22:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857751-GermlineCNVCaller-BETA 2019-11-25T20:18:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857771-CallCopyRatioSegments-BETA 2019-11-25T20:19:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857791-ScatterIntervalsByNs-Picard 2019-11-25T20:22:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857811-AS-InbreedingCoeff 2019-11-25T20:22:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857831-PlatformReadFilter 2019-11-25T20:19:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857851-BamIndexStats-Picard 2019-11-25T20:22:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857871-FilterMutectCalls 2019-11-25T20:22:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857891-AddOrReplaceReadGroups-Picard 2019-11-25T20:19:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857911-PlotModeledSegments-BETA 2019-11-25T20:19:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857931-CollectVariantCallingMetrics-Picard 2019-11-25T20:19:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857951-CombineGVCFs 2019-11-25T20:22:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857971-CollectGcBiasMetrics-Picard 2019-11-25T20:19:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036857991-LiftoverVcf-Picard 2019-11-25T20:22:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858011-MateOnSameContigOrNoMappedMateReadFilter 2019-11-25T20:22:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858031-ReadStrandFilter 2019-11-25T20:19:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858051-ApplyBQSRSpark-BETA 2019-11-25T20:22:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858071-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T20:19:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858091-CalculateGenotypePosteriors 2019-11-25T20:22:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858111-MergeVcfs-Picard 2019-11-25T20:22:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858131-CollectAllelicCounts-BETA 2019-11-25T20:22:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858151-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T20:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858171-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T20:22:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858191-PreprocessIntervals-BETA 2019-11-25T20:22:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858211-QualityScoreDistribution-Picard 2019-11-25T20:19:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858231-CombineSegmentBreakpoints-EXPERIMENTAL 2019-11-25T20:22:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858251-FlagStat 2019-11-25T20:22:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858271-BaitDesigner-Picard 2019-11-25T20:22:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858291-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T20:22:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858311-FixMateInformation-Picard 2019-11-25T20:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858331-SortVcf-Picard 2019-11-25T20:22:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858351-PrintVariantsSpark-BETA 2019-11-25T20:22:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858371-ValidateSamFile-Picard 2019-11-25T20:22:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858391-FastqToSam-Picard 2019-11-25T20:22:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858411-SortSam-Picard 2019-11-25T20:22:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858431-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T20:19:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858451-FuncotatorDataSourceDownloader-BETA 2019-11-25T20:19:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858471-StrandArtifact 2019-11-25T20:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858491-AnnotateIntervals-BETA 2019-11-25T20:23:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858511-RevertSam-Picard 2019-11-25T20:23:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858551-CollectFragmentCounts-BETA 2019-11-25T20:23:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858571-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T20:23:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858591-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T20:23:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858611-ReadPosRankSumTest 2019-11-25T20:19:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858631-BaseQuality 2019-11-25T20:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858651-SeqIsStoredReadFilter 2019-11-25T20:19:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858671-IntervalOverlapReadFilter 2019-11-25T20:19:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858691-VariantRecalibrator 2019-11-25T20:23:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858711-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T20:23:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858731-PlotDenoisedCopyRatios-BETA 2019-11-25T20:19:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858751-SplitIntervals 2019-11-25T20:23:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858771-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T20:23:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858791-EvaluateInfoFieldConcordance-BETA 2019-11-25T20:23:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858811-SplitNCigarReads 2019-11-25T20:23:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858831-NonZeroFragmentLengthReadFilter 2019-11-25T20:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858851-ProperlyPairedReadFilter 2019-11-25T20:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858871-FilterFuncotations-EXPERIMENTAL 2019-11-25T20:23:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858891-CNNVariantTrain-EXPERIMENTAL 2019-11-25T20:23:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858911-GenotypeGVCFs 2019-11-25T20:23:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858931-AS-BaseQualityRankSumTest 2019-11-25T20:23:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858951-Concordance-BETA 2019-11-25T20:23:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858971-FragmentLengthReadFilter 2019-11-25T20:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036858991-BuildBamIndex-Picard 2019-11-25T20:23:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859011-CollectRrbsMetrics-Picard 2019-11-25T20:20:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859031-NotSecondaryAlignmentReadFilter 2019-11-25T20:20:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859051-ReferenceBases 2019-11-25T20:20:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859071-ValidAlignmentEndReadFilter 2019-11-25T20:23:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859091-QualityScoreDistributionSpark-BETA 2019-11-25T20:23:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859111-DepthPerSampleHC 2019-11-25T20:23:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859131-AlleleFraction 2019-11-25T20:23:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859151-RenameSampleInVcf-Picard 2019-11-25T20:23:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859171-MappingQualityAvailableReadFilter 2019-11-25T20:20:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859191-CollectOxoGMetrics-Picard 2019-11-25T20:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859211-CreateReadCountPanelOfNormals-BETA 2019-11-25T20:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859231-CountReadsSpark-BETA 2019-11-25T20:23:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859251-ASEReadCounter 2019-11-25T20:23:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859271-GtcToVcf-Picard 2019-11-25T20:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036859291-CheckTerminatorBlock-Picard 2019-11-25T20:20:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861091-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-11-25T21:00:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861111-ChromosomeCounts 2019-11-25T21:00:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861131-LibraryReadFilter 2019-11-25T21:00:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861151-NonChimericOriginalAlignmentReadFilter 2019-11-25T21:00:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861171-MeanQualityByCycle-Picard 2019-11-25T21:05:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861191-Pileup 2019-11-25T21:05:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861211-OverclippedReadFilter 2019-11-25T21:01:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861231-BwaMemIndexImageCreator 2019-11-25T21:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861251-WellformedReadFilter 2019-11-25T21:05:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861271-SampleReadFilter 2019-11-25T21:01:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861291-AnalyzeCovariates 2019-11-25T21:05:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861311-FirstOfPairReadFilter 2019-11-25T21:01:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861331-Funcotator-BETA 2019-11-25T21:05:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861351-CollectQualityYieldMetrics-Picard 2019-11-25T21:01:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861371-PathSeqPipelineSpark 2019-11-25T21:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861391-CalcMetadataSpark-BETA 2019-11-25T21:05:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861411-SecondOfPairReadFilter 2019-11-25T21:01:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861431-AlignmentAgreesWithHeaderReadFilter 2019-11-25T21:01:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861451-AS-StrandOddsRatio 2019-11-25T21:05:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861471-AnnotatePairOrientation-BETA 2019-11-25T21:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861491-CountReads 2019-11-25T21:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861511-FixVcfHeader-Picard 2019-11-25T21:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861531-CollectHsMetrics-Picard 2019-11-25T21:05:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861551-EstimateLibraryComplexity-Picard 2019-11-25T21:05:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861571-ViewSam-Picard 2019-11-25T21:05:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861591-AnnotateVcfWithExpectedAlleleFraction 2019-11-25T21:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861611-CountVariants 2019-11-25T21:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861651-BamToBfq-Picard 2019-11-25T21:01:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861671-VariantAnnotator-BETA 2019-11-25T21:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861691-PrimaryLineReadFilter 2019-11-25T21:01:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861711-CheckFingerprint-Picard 2019-11-25T21:01:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861731-FindBreakpointEvidenceSpark-BETA 2019-11-25T21:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861751-UniqueAltReadCount 2019-11-25T21:01:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861771-MappingQuality 2019-11-25T21:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861791-QualByDepth 2019-11-25T21:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861811-VariantsToTable 2019-11-25T21:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861831-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2019-11-25T21:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861851-CountVariantsSpark-BETA 2019-11-25T21:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861871-ClusterCrosscheckMetrics-Picard 2019-11-25T21:01:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861891-ClipReads 2019-11-25T21:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861911-CollectSamErrorMetrics-Picard 2019-11-25T21:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036861971-SoftClippedReadFilter 2019-11-25T21:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862051-DepthPerAlleleBySample 2019-11-25T21:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862071-CalculateReadGroupChecksum-Picard 2019-11-25T21:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862091-SetNmMdAndUqTags-Picard 2019-11-25T21:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862111-FuncotateSegments-BETA 2019-11-25T21:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862151-GatherBamFiles-Picard 2019-11-25T21:01:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862171-CalculateFingerprintMetrics-Picard 2019-11-25T21:01:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862191-PathSeqBuildReferenceTaxonomy 2019-11-25T21:01:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862211-AS-FisherStrand 2019-11-25T21:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862231-AnnotateVcfWithBamDepth 2019-11-25T21:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862271-PathSeqBuildKmers 2019-11-25T21:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862291-MakeSitesOnlyVcf-Picard 2019-11-25T21:06:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862311-IntervalListTools-Picard 2019-11-25T21:06:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862331-StrandBiasBySample 2019-11-25T21:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862351-FilterIntervals-BETA 2019-11-25T21:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862371-MappingQualityRankSumTest 2019-11-25T21:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862391-CollectJumpingLibraryMetrics-Picard 2019-11-25T21:02:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862411-SplitSamByNumberOfReads-Picard 2019-11-25T21:06:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862431-CalculateMixingFractions 2019-11-25T21:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862451-AccumulateVariantCallingMetrics-Picard 2019-11-25T21:02:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862471-IlluminaBasecallsToSam-Picard 2019-11-25T21:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862491-GenomicsDBImport 2019-11-25T21:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862511-PlatformUnitReadFilter 2019-11-25T21:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862531-OxoGReadCounts 2019-11-25T21:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862551-PrintReads 2019-11-25T21:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862571-ReplaceSamHeader-Picard 2019-11-25T21:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862591-CountFalsePositives-BETA 2019-11-25T21:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862611-CollectIlluminaLaneMetrics-Picard 2019-11-25T21:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862631-CountBasesInReference 2019-11-25T21:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862651-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T21:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862671-PathSeqBwaSpark 2019-11-25T21:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862691-MarkIlluminaAdapters-Picard 2019-11-25T21:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862711-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T21:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862731-CheckIlluminaDirectory-Picard 2019-11-25T21:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862751-CollectBaseDistributionByCycle-Picard 2019-11-25T21:02:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862771-MergeBamAlignment-Picard 2019-11-25T21:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862791-FixMisencodedBaseQualityReads 2019-11-25T21:07:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862811-LeftAlignAndTrimVariants 2019-11-25T21:07:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862831-RevertSamSpark-BETA 2019-11-25T21:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862851-ExtractIlluminaBarcodes-Picard 2019-11-25T21:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862871-RemoveNearbyIndels 2019-11-25T21:07:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862891-CompareDuplicatesSpark-BETA 2019-11-25T21:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862911-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T21:07:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862931-MarkDuplicates-Picard 2020-06-18T02:11:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862951-CreateSequenceDictionary-Picard 2019-11-25T21:07:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862971-ReorderSam-Picard 2019-11-25T21:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036862991-GenotypeSummaries 2019-11-25T21:03:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863011-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T21:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863031-CollectWgsMetrics-Picard 2019-11-25T21:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863071-AS-ReadPosRankSumTest 2019-11-25T21:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863091-GetPileupSummaries-BETA 2019-11-25T21:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863111-FifoBuffer-Picard 2019-11-25T21:03:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863131-VariantFiltration 2019-11-25T21:07:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863151-BaseRecalibrator 2019-11-25T21:07:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863171-RevertBaseQualityScores 2019-11-25T21:07:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863191-ClippingRankSumTest 2019-11-25T21:03:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863211-EstimateLibraryComplexityGATK-BETA 2019-11-25T21:07:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863231-BaseQualityRankSumTest 2019-11-25T21:03:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863251-GermlineCNVCaller-BETA 2019-11-25T21:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863291-UpdateVcfSequenceDictionary-Picard 2019-11-25T21:03:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863331-ReadNameReadFilter 2019-11-25T21:03:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863351-CallCopyRatioSegments-BETA 2019-11-25T21:03:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863371-AS-InbreedingCoeff 2019-11-25T21:07:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863391-PlatformReadFilter 2019-11-25T21:03:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863411-VcfFormatConverter-Picard 2019-11-25T21:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863431-PlotModeledSegments-BETA 2019-11-25T21:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863451-CollectVariantCallingMetrics-Picard 2019-11-25T21:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863471-CombineGVCFs 2019-11-25T21:07:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863491-CollectGcBiasMetrics-Picard 2019-11-25T21:03:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863511-LiftoverVcf-Picard 2019-11-25T21:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863531-Coverage 2019-11-25T21:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863551-ApplyBQSRSpark-BETA 2019-11-25T21:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863571-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-11-25T21:04:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863591-ValidateVariants 2019-11-25T21:07:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863611-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-11-25T21:04:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863631-QualityScoreDistribution-Picard 2019-11-25T21:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863651-FlagStat 2019-11-25T21:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863671-BaitDesigner-Picard 2019-11-25T21:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863691-InbreedingCoeff 2019-11-25T21:04:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863711-FixMateInformation-Picard 2019-11-25T21:04:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863731-PrintVariantsSpark-BETA 2019-11-25T21:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863751-ValidateSamFile-Picard 2019-11-25T21:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863771-SamToFastq-Picard 2019-11-25T21:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863791-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T21:04:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863811-FuncotatorDataSourceDownloader-BETA 2019-11-25T21:04:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863831-StrandArtifact 2019-11-25T21:04:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863851-GatherVcfsCloud-BETA 2019-11-25T21:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863871-AnnotateIntervals-BETA 2019-11-25T21:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863891-PathSeqScoreSpark 2019-11-25T21:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863911-RevertSam-Picard 2019-11-25T21:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863931-PassesVendorQualityCheckReadFilter 2019-11-25T21:04:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863951-AS-MappingQualityRankSumTest 2019-11-25T21:08:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863971-CollectFragmentCounts-BETA 2019-11-25T21:08:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036863991-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T21:08:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864011-BaseRecalibratorSparkSharded-EXPERIMENTAL 2019-11-25T21:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864031-ReadPosRankSumTest 2019-11-25T21:04:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864051-BaseQuality 2019-11-25T21:04:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864071-IntervalOverlapReadFilter 2019-11-25T21:04:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864091-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T21:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864111-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T21:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864131-PathSeqFilterSpark 2019-11-25T21:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864151-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-11-25T21:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864171-FastaAlternateReferenceMaker 2019-11-25T21:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864191-UnmarkDuplicates 2019-11-25T21:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864211-StructuralVariationDiscoveryPipelineSpark-BETA 2019-11-25T21:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864231-SplitNCigarReads 2019-11-25T21:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864251-NonZeroFragmentLengthReadFilter 2019-11-25T21:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864271-PileupSpark-BETA 2019-11-25T21:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864291-ProperlyPairedReadFilter 2019-11-25T21:04:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864311-SplitVcfs-Picard 2019-11-25T21:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864331-SplitSamByLibrary-Picard 2019-11-25T21:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864351-CrosscheckFingerprints-Picard 2019-11-25T21:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864371-CNNVariantTrain-EXPERIMENTAL 2019-11-25T21:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864391-GenotypeGVCFs 2019-11-25T21:08:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864411-AddCommentsToBam-Picard 2019-11-25T21:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864431-AnalyzeSaturationMutagenesis-BETA 2019-11-25T21:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864451-AS-BaseQualityRankSumTest 2019-11-25T21:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864471-FragmentLengthReadFilter 2019-11-25T21:05:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864491-BuildBamIndex-Picard 2019-11-25T21:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864511-CollectRrbsMetrics-Picard 2019-11-25T21:05:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864531-NotSecondaryAlignmentReadFilter 2019-11-25T21:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864551-FindMendelianViolations-Picard 2019-11-25T21:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864571-ReferenceBases 2019-11-25T21:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864591-MetricsReadFilter 2019-11-25T21:05:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864611-ValidAlignmentEndReadFilter 2019-11-25T21:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864631-QualityScoreDistributionSpark-BETA 2019-11-25T21:08:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864651-DepthPerSampleHC 2019-11-25T21:08:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864671-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T21:05:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864691-OrientationBiasReadCounts 2019-11-25T21:05:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864711-CountNs 2019-11-25T21:05:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864731-RenameSampleInVcf-Picard 2019-11-25T21:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864751-MappingQualityAvailableReadFilter 2019-11-25T21:05:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864771-CountReadsSpark-BETA 2019-11-25T21:08:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864791-PrintReadsSpark-BETA 2019-11-25T21:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864831-ASEReadCounter 2019-11-25T21:08:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864851-FilterVariantTranches-EXPERIMENTAL 2019-11-25T21:08:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864871-GtcToVcf-Picard 2019-11-25T21:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036864891-CheckTerminatorBlock-Picard 2019-11-25T21:05:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882271-MeanQualityByCycle-Picard 2019-11-25T22:38:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882291-CollectHiSeqXPfFailMetrics-Picard 2019-11-25T22:38:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882311-GenotypeConcordance-Picard 2019-11-25T22:38:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882331-SampleReadFilter 2019-11-25T22:34:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882351-RMSMappingQuality 2019-11-25T22:38:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882371-CollectQualityYieldMetrics-Picard 2019-11-25T22:34:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882391-PathSeqPipelineSpark 2019-11-25T22:38:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882411-CalcMetadataSpark-BETA 2019-11-25T22:38:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882431-AS-StrandOddsRatio 2019-11-25T22:38:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882451-FilterVcf-Picard 2019-11-25T22:34:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882471-VariantEval-BETA 2019-11-25T22:38:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882491-CountReads 2019-11-25T22:38:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882511-FixVcfHeader-Picard 2019-11-25T22:38:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882531-GnarlyGenotyper-BETA 2019-11-25T22:38:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882551-AllowAllReadsReadFilter 2019-11-25T22:34:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882571-NotDuplicateReadFilter 2019-11-25T22:34:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882591-BamToBfq-Picard 2019-11-25T22:34:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882611-FilterSamReads-Picard 2019-11-25T22:38:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882631-PrimaryLineReadFilter 2019-11-25T22:34:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882651-StrandOddsRatio 2019-11-25T22:38:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882671--Tool-Documentation-Index 2019-12-16T20:19:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882691-CheckFingerprint-Picard 2019-11-25T22:34:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882711-HasReadGroupReadFilter 2019-11-25T22:34:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882731-DetermineGermlineContigPloidy-BETA 2019-11-25T22:34:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882751-FindBreakpointEvidenceSpark-BETA 2019-11-25T22:38:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882771-MappingQuality 2019-11-25T22:34:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882811-VariantsToTable 2019-11-25T22:38:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882831-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2019-11-25T22:38:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882851-NormalizeFasta-Picard 2019-11-25T22:38:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882871-CNNVariantWriteTensors-EXPERIMENTAL 2019-11-25T22:38:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882891-UpdateVCFSequenceDictionary 2019-11-25T22:38:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882911-IlluminaBasecallsToFastq-Picard 2019-11-25T22:38:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882931-SamFormatConverter-Picard 2019-11-25T22:34:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882951-FisherStrand 2019-11-25T22:38:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882971-ClipReads 2019-11-25T22:38:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036882991-GetSampleName-BETA 2019-11-25T22:38:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883011-CalculateReadGroupChecksum-Picard 2019-11-25T22:38:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883031-CompareMetrics-Picard 2019-11-25T22:38:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883051-GatherBamFiles-Picard 2019-11-25T22:34:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883071-CompareBaseQualities 2019-11-25T22:34:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883091-BwaSpark-BETA 2019-11-25T22:39:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883111-CollectAlignmentSummaryMetrics-Picard 2019-11-25T22:35:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883131-AnnotateVcfWithBamDepth 2019-11-25T22:39:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883151-CollectSequencingArtifactMetrics-Picard 2019-11-25T22:35:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883171-MappedReadFilter 2019-11-25T22:35:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883211-GatherBQSRReports 2019-11-25T22:35:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883231-CalculateContamination 2019-11-25T22:39:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883251-ApplyBQSR 2019-11-25T22:39:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883271-MakeSitesOnlyVcf-Picard 2019-11-25T22:39:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883291-StrandBiasBySample 2019-11-25T22:39:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883311-FilterIntervals-BETA 2019-11-25T22:35:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883331-CollectJumpingLibraryMetrics-Picard 2019-11-25T22:35:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883351-SplitSamByNumberOfReads-Picard 2019-11-25T22:39:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883391-CalculateMixingFractions 2019-11-25T22:39:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883411-SelectVariants 2019-11-25T22:39:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883431-AccumulateVariantCallingMetrics-Picard 2019-11-25T22:35:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883451-ReadGroupReadFilter 2019-11-25T22:35:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883471-MappingQualityReadFilter 2019-11-25T22:39:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883491-GenomicsDBImport 2025-06-20T07:33:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883511-CollectQualityYieldMetricsSpark-BETA 2019-11-25T22:39:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883531-PlatformUnitReadFilter 2019-11-25T22:35:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883551-OxoGReadCounts 2019-11-25T22:35:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883571-PrintReads 2019-11-25T22:39:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883591-CrosscheckReadGroupFingerprints-Picard 2019-11-25T22:35:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883611-ValidAlignmentStartReadFilter 2019-11-25T22:39:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883631-ReadsPipelineSpark-BETA 2019-11-25T22:39:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883651-CollectIlluminaLaneMetrics-Picard 2019-11-25T22:39:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883671-PolymorphicNuMT 2019-11-25T22:35:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883691-MarkDuplicatesGATK-EXPERIMENTAL 2019-11-25T22:39:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883711-SetNmAndUqTags-Picard 2019-11-25T22:39:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883731-PathSeqBwaSpark 2019-11-25T22:39:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883751-SampleList 2019-11-25T22:35:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883771-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-11-25T22:39:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883791-MeanQualityByCycleSpark-BETA 2019-11-25T22:39:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883811-FragmentLength 2019-11-25T22:35:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883831-CheckIlluminaDirectory-Picard 2019-11-25T22:39:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883851-CollectTargetedPcrMetrics-Picard 2019-11-25T22:39:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883871-MergeBamAlignment-Picard 2019-11-25T22:35:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883891-FixMisencodedBaseQualityReads 2019-11-25T22:39:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883911-RevertSamSpark-BETA 2019-11-25T22:39:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883931-BedToIntervalList-Picard 2019-11-25T22:39:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883951-CompareDuplicatesSpark-BETA 2019-11-25T22:39:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883971-CollectRawWgsMetrics-Picard 2019-11-25T22:39:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036883991-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-11-25T22:39:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884011-MarkDuplicates-Picard 2019-11-25T22:39:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884031-VcfToAdpc-Picard 2019-11-25T22:36:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884051-GenotypeSummaries 2019-11-25T22:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884071-FilterAlignmentArtifacts-EXPERIMENTAL 2019-11-25T22:39:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884091-CollectWgsMetrics-Picard 2019-11-25T22:39:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884111-FifoBuffer-Picard 2019-11-25T22:36:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884131-BaseRecalibrator 2019-11-25T22:39:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884151-GatherTranches-BETA 2019-11-25T22:36:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884171-BQSRPipelineSpark-BETA 2019-11-25T22:39:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884191-IntervalListToBed-Picard 2019-11-25T22:36:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884211-ApplyVQSR 2019-11-25T22:40:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884231-UpdateVcfSequenceDictionary-Picard 2019-11-25T22:36:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884251-MappingQualityZero 2019-11-25T22:40:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884271-CallCopyRatioSegments-BETA 2019-11-25T22:36:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884291-ScatterIntervalsByNs-Picard 2019-11-25T22:40:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884311-AS-InbreedingCoeff 2019-11-25T22:40:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884331-PlatformReadFilter 2019-11-25T22:36:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884351-BamIndexStats-Picard 2019-11-25T22:40:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884371-FilterMutectCalls 2019-11-25T22:40:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884391-AddOrReplaceReadGroups-Picard 2019-11-25T22:36:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884411-CollectVariantCallingMetrics-Picard 2019-11-25T22:36:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884431-LiftoverVcf-Picard 2019-11-25T22:40:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884451-Coverage 2019-11-25T22:40:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884471-ApplyBQSRSpark-BETA 2019-11-25T22:40:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884491-ExtractSVEvidenceSpark-BETA 2019-11-25T22:40:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884511-MethylationTypeCaller-EXPERIMENTAL 2019-11-25T22:40:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884531-PreprocessIntervals-BETA 2019-11-25T22:40:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884551-FlagStat 2019-11-25T22:40:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884571-BaitDesigner-Picard 2019-11-25T22:40:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884591-ReadLengthEqualsCigarLengthReadFilter 2019-11-25T22:40:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884611-FixMateInformation-Picard 2019-11-25T22:37:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884631-PrintVariantsSpark-BETA 2019-11-25T22:40:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884651-ValidateSamFile-Picard 2019-11-25T22:40:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884671-CollectIlluminaBasecallingMetrics-Picard 2019-11-25T22:37:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884691-FuncotatorDataSourceDownloader-BETA 2019-11-25T22:37:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884711-MergeSamFiles-Picard 2019-11-25T22:40:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884731-CollectRnaSeqMetrics-Picard 2019-11-25T22:37:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884751-GatherVcfsCloud-BETA 2019-11-25T22:40:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884771-AnnotateIntervals-BETA 2019-11-25T22:40:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884791-PathSeqScoreSpark 2019-11-25T22:40:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884811-PassesVendorQualityCheckReadFilter 2019-11-25T22:37:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884831-SplitReads 2019-11-25T22:40:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884851-CollectFragmentCounts-BETA 2019-11-25T22:40:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884871-FixCallSetSampleOrdering-EXPERIMENTAL 2019-11-25T22:40:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884891-ReadPosRankSumTest 2019-11-25T22:37:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884911-IntervalOverlapReadFilter 2019-11-25T22:37:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884931-NonZeroReferenceLengthAlignmentReadFilter 2019-11-25T22:37:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884951-CollectBaseDistributionByCycleSpark-BETA 2019-11-25T22:40:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884971-PathSeqFilterSpark 2019-11-25T22:40:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036884991-SplitIntervals 2019-11-25T22:40:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885011-SplitNCigarReads 2019-11-25T22:40:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885031-NonZeroFragmentLengthReadFilter 2019-11-25T22:37:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885051-PileupSpark-BETA 2019-11-25T22:40:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885071-SplitVcfs-Picard 2019-11-25T22:40:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885091-CrosscheckFingerprints-Picard 2019-11-25T22:40:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885111-FindBadGenomicKmersSpark-BETA 2019-11-25T22:40:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885131-AS-QualByDepth 2019-11-25T22:40:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885151-Concordance-BETA 2019-11-25T22:40:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885171-FragmentLengthReadFilter 2019-11-25T22:37:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885191-BuildBamIndex-Picard 2019-11-25T22:40:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885211-CollectRrbsMetrics-Picard 2019-11-25T22:37:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885231-ReferenceBases 2019-11-25T22:37:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885251-ValidAlignmentEndReadFilter 2019-11-25T22:41:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885271-FastaReferenceMaker 2019-11-25T22:41:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885291-DepthPerSampleHC 2019-11-25T22:41:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885311-AlleleFraction 2019-11-25T22:41:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885331-ConvertSequencingArtifactToOxoG-Picard 2019-11-25T22:38:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885351-OrientationBiasReadCounts 2019-11-25T22:38:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885371-MappingQualityAvailableReadFilter 2019-11-25T22:38:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885391-CreateReadCountPanelOfNormals-BETA 2019-11-25T22:38:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885411-CountReadsSpark-BETA 2019-11-25T22:41:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885431-CountBasesSpark-BETA 2019-11-25T22:41:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885451-PrintReadsSpark-BETA 2019-11-25T22:41:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885471-ASEReadCounter 2019-11-25T22:41:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885491-FilterVariantTranches-EXPERIMENTAL 2019-11-25T22:41:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885511-CreateSomaticPanelOfNormals-BETA 2019-11-25T22:41:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885531-GtcToVcf-Picard 2019-11-25T22:38:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885551-ReadLengthReadFilter 2019-11-25T22:38:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036885571-CleanSam-Picard 2019-11-25T22:38:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036887972-MeanQualityByCycle-Picard 2020-01-07T20:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036887992-CollectHiSeqXPfFailMetrics-Picard 2020-01-07T20:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888012-GenotypeConcordance-Picard 2020-01-07T20:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888032-Pileup 2020-01-07T20:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888052-BwaMemIndexImageCreator 2020-01-07T20:52:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888072-WellformedReadFilter 2020-01-07T20:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888092-AnalyzeCovariates 2020-01-07T20:51:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888112-Funcotator-BETA 2020-01-07T20:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888132-PathSeqPipelineSpark 2020-01-07T20:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888152-SecondOfPairReadFilter 2020-01-07T20:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888172-AlignmentAgreesWithHeaderReadFilter 2020-01-07T20:51:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888192-AS-StrandOddsRatio 2020-01-07T20:52:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888212-FilterVcf-Picard 2020-01-07T20:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888232-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-01-07T20:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888252-CountReads 2020-01-07T20:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888272-EstimateLibraryComplexity-Picard 2020-01-07T20:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888292-ViewSam-Picard 2020-01-07T20:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888312-AllowAllReadsReadFilter 2020-01-07T20:51:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888332-LiftOverIntervalList-Picard 2020-01-07T20:54:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888352-BamToBfq-Picard 2020-01-07T20:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888372-PrimaryLineReadFilter 2020-01-07T20:55:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888392-CheckFingerprint-Picard 2020-01-07T20:52:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888412-HasReadGroupReadFilter 2020-01-07T20:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888432-DetermineGermlineContigPloidy-BETA 2020-01-07T20:53:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888452-FindBreakpointEvidenceSpark-BETA 2020-01-07T20:53:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888472-MappingQuality 2020-01-07T20:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888492-VariantsToTable 2020-01-07T20:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888512-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T20:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888532-UpdateVCFSequenceDictionary 2020-01-07T20:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888552-IlluminaBasecallsToFastq-Picard 2020-01-07T20:54:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888572-FisherStrand 2020-01-07T20:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888592-ClusterCrosscheckMetrics-Picard 2020-01-07T20:52:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888612-ClipReads 2020-01-07T20:52:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888632-CollectSamErrorMetrics-Picard 2020-01-07T20:52:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888652-SoftClippedReadFilter 2020-01-07T20:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888672-GetSampleName-BETA 2020-01-07T20:54:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888692-DepthPerAlleleBySample 2020-01-07T20:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888712-CalculateReadGroupChecksum-Picard 2020-01-07T20:52:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888732-SortReadFileSpark-BETA 2020-01-07T20:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888752-CompareMetrics-Picard 2020-01-07T20:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888772-FuncotateSegments-BETA 2020-01-07T20:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888792-CalculateFingerprintMetrics-Picard 2020-01-07T20:52:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888812-AS-FisherStrand 2020-01-07T20:52:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888832-CompareBaseQualities 2020-01-07T20:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888852-BwaSpark-BETA 2020-01-07T20:52:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888872-CollectAlignmentSummaryMetrics-Picard 2020-01-07T20:52:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888892-GatherVcfs-Picard 2020-01-07T20:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888912-MappedReadFilter 2020-01-07T20:54:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888932-MarkDuplicatesWithMateCigar-Picard 2020-01-07T20:54:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888952-GatherBQSRReports 2020-01-07T20:53:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888972-CalculateContamination 2021-02-04T19:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036888992-CpxVariantReInterpreterSpark-BETA 2020-01-07T20:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889012-PathSeqBuildKmers 2020-01-07T20:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889032-MakeSitesOnlyVcf-Picard 2020-01-07T20:54:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889052-IntervalListTools-Picard 2020-01-07T20:54:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889072-StrandBiasBySample 2020-01-07T20:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889092-MappingQualityRankSumTest 2020-01-07T20:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889132-FilterMutectCalls 2020-01-07T20:53:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889152-CalculateMixingFractions 2020-01-07T20:52:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889172-IlluminaBasecallsToSam-Picard 2020-01-07T20:54:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889192-MappingQualityReadFilter 2020-01-07T20:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889212-GenomicsDBImport 2020-01-07T20:53:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889232-CollectQualityYieldMetricsSpark-BETA 2020-01-07T20:52:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889252-OxoGReadCounts 2020-01-07T20:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889272-PrintReads 2020-01-07T20:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889292-CrosscheckReadGroupFingerprints-Picard 2020-01-07T20:53:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889312-HaplotypeCaller 2020-01-07T20:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889332-MateUnmappedAndUnmappedReadFilter 2020-01-07T20:54:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889352-VcfToIntervalList-Picard 2020-01-07T20:55:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889372-SetNmAndUqTags-Picard 2020-01-07T20:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889392-MarkIlluminaAdapters-Picard 2020-01-07T20:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889412-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-01-07T20:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889432-ReblockGVCF-EXPERIMENTAL 2020-01-07T20:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889452-MergeBamAlignment-Picard 2020-01-07T20:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889472-LeftAlignAndTrimVariants 2020-01-07T20:54:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889492-ExtractIlluminaBarcodes-Picard 2020-01-07T20:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889512-BedToIntervalList-Picard 2020-01-07T20:52:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889532-RemoveNearbyIndels 2020-01-07T20:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889552-CompareDuplicatesSpark-BETA 2020-01-07T20:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889572-FilterByOrientationBias-EXPERIMENTAL 2020-01-07T20:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889592-MarkDuplicates-Picard 2020-01-07T20:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889612-CreateSequenceDictionary-Picard 2020-01-07T20:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889632-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T20:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889652-PostprocessGermlineCNVCalls-BETA 2020-01-07T20:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889672-AS-ReadPosRankSumTest 2020-01-07T20:52:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889692-FifoBuffer-Picard 2020-01-07T20:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889712-VariantFiltration 2020-01-07T20:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889732-BQSRPipelineSpark-BETA 2020-01-07T20:52:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889752-EstimateLibraryComplexityGATK-BETA 2020-01-07T20:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889772-PossibleDeNovo 2020-01-07T20:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889792-CollectInsertSizeMetricsSpark-BETA 2020-01-07T20:52:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889812-BaseQualityRankSumTest 2020-01-07T20:52:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889832-ApplyVQSR 2020-01-07T20:52:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889852-GermlineCNVCaller-BETA 2020-01-07T20:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889872-UpdateVcfSequenceDictionary-Picard 2020-01-07T20:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889892-ReadNameReadFilter 2020-01-07T20:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889912-ScatterIntervalsByNs-Picard 2020-01-07T20:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889932-AS-InbreedingCoeff 2020-01-07T20:52:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889952-VcfFormatConverter-Picard 2020-01-07T20:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889972-AddOrReplaceReadGroups-Picard 2020-01-07T20:51:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036889992-CombineGVCFs 2020-01-07T20:52:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890012-CollectGcBiasMetrics-Picard 2020-01-07T20:52:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890032-AddOATag-Picard 2020-01-07T20:51:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890052-ReadPosition 2020-01-07T20:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890072-ApplyBQSRSpark-BETA 2020-01-07T20:52:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890092-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-01-07T20:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890112-CalculateGenotypePosteriors 2020-01-07T20:52:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890132-ValidateVariants 2020-01-07T20:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890152-ExtractSVEvidenceSpark-BETA 2020-01-07T20:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890172-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-01-07T20:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890192-MethylationTypeCaller-EXPERIMENTAL 2020-01-07T20:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890212-BaitDesigner-Picard 2020-01-07T20:52:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890232-ReadLengthEqualsCigarLengthReadFilter 2020-01-07T20:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890252-SortVcf-Picard 2020-01-07T20:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890272-FastqToSam-Picard 2020-01-07T20:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890292-SamToFastq-Picard 2020-01-07T20:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890312-SortSam-Picard 2020-01-07T20:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890332-CollectIlluminaBasecallingMetrics-Picard 2020-01-07T20:52:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890352-StrandArtifact 2020-01-07T20:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890372-CollectRnaSeqMetrics-Picard 2020-01-07T20:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890392-GatherVcfsCloud-BETA 2020-01-07T20:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890412-PathSeqScoreSpark 2020-01-07T20:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890432-RevertSam-Picard 2020-01-07T20:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890452-PassesVendorQualityCheckReadFilter 2020-01-07T20:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890472-SplitReads 2020-01-07T20:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890492-AS-MappingQualityRankSumTest 2020-01-07T20:52:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890512-FixCallSetSampleOrdering-EXPERIMENTAL 2020-01-07T20:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890532-ReadPosRankSumTest 2020-01-07T20:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890552-IntervalOverlapReadFilter 2020-01-07T20:54:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890572-CollectBaseDistributionByCycleSpark-BETA 2020-01-07T20:52:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890592-PathSeqFilterSpark 2020-01-07T20:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890612-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-01-07T20:53:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890632-FastaAlternateReferenceMaker 2020-01-07T20:53:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890652-UnmarkDuplicates 2020-01-07T20:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890672-StructuralVariationDiscoveryPipelineSpark-BETA 2020-01-07T20:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890692-NonZeroFragmentLengthReadFilter 2020-01-07T20:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890712-CigarContainsNoNOperator 2020-01-07T20:52:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890732-SplitVcfs-Picard 2020-01-07T20:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890752-SplitSamByLibrary-Picard 2020-01-07T20:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890772-CrosscheckFingerprints-Picard 2020-01-07T20:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890792-CNNVariantTrain-EXPERIMENTAL 2020-01-07T20:52:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890812-TandemRepeat 2020-01-07T20:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890832-FindBadGenomicKmersSpark-BETA 2020-01-07T20:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890852-Concordance-BETA 2020-01-07T20:53:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890872-CollectRrbsMetrics-Picard 2020-01-07T20:52:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890892-FindMendelianViolations-Picard 2020-01-07T20:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890912-MetricsReadFilter 2020-01-07T20:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890932-ValidAlignmentEndReadFilter 2020-01-07T20:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036890952-FastaReferenceMaker 2020-01-07T20:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891012-DepthPerSampleHC 2020-01-07T20:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891032-AlleleFraction 2020-01-07T20:51:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891052-ConvertSequencingArtifactToOxoG-Picard 2020-01-07T20:53:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891072-OrientationBiasReadCounts 2020-01-07T20:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891092-RenameSampleInVcf-Picard 2020-01-07T20:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891112-CountReadsSpark-BETA 2020-01-07T20:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891132-PrintReadsSpark-BETA 2020-01-07T20:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891152-FilterVariantTranches-EXPERIMENTAL 2020-01-07T20:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891192-CreateSomaticPanelOfNormals-BETA 2020-01-07T20:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891212-GtcToVcf-Picard 2020-01-07T20:54:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891232-CheckTerminatorBlock-Picard 2020-01-07T20:52:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036891252-CleanSam-Picard 2020-01-07T20:52:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896152-ChromosomeCounts 2020-01-07T20:43:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896172-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2020-01-07T20:44:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896192-MeanQualityByCycle-Picard 2020-01-07T20:50:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896212-CollectHiSeqXPfFailMetrics-Picard 2020-01-07T20:44:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896232-Pileup 2020-01-07T20:50:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896252-SampleReadFilter 2020-01-07T20:51:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896272-AnalyzeCovariates 2020-01-07T20:43:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896292-RMSMappingQuality 2020-01-07T20:51:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896312-FirstOfPairReadFilter 2020-01-07T20:49:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896332-Funcotator-BETA 2020-01-07T20:49:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896352-CollectQualityYieldMetrics-Picard 2020-01-07T20:44:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896372-SecondOfPairReadFilter 2020-01-07T20:51:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896392-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-01-07T20:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896432-VariantEval-BETA 2020-01-07T20:51:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896472-FixVcfHeader-Picard 2020-01-07T20:49:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896512-EstimateLibraryComplexity-Picard 2020-01-07T20:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896552-ViewSam-Picard 2020-01-07T20:51:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896612-CountVariants 2020-01-07T20:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896652-NotDuplicateReadFilter 2020-01-07T20:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896692-FilterSamReads-Picard 2020-01-07T20:49:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896712-PrimaryLineReadFilter 2020-01-07T20:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896772--Tool-Documentation-Index 2020-01-07T20:41:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896792-CheckFingerprint-Picard 2020-01-07T20:43:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896812-HasReadGroupReadFilter 2020-01-07T20:49:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896832-DetermineGermlineContigPloidy-BETA 2020-01-07T20:49:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896852-UniqueAltReadCount 2020-01-07T20:51:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896872-QualByDepth 2020-01-07T20:50:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable 2024-11-10T01:46:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896912-AS-RMSMappingQuality 2020-01-07T20:43:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896932-IlluminaBasecallsToFastq-Picard 2020-01-07T20:49:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896952-FisherStrand 2020-01-07T20:49:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896972-SoftClippedReadFilter 2020-01-07T20:51:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036896992-GetSampleName-BETA 2020-01-07T20:49:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897012-MarkDuplicatesSpark-BETA 2020-01-07T20:50:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897032-DepthPerAlleleBySample 2020-01-07T20:49:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897052-GatherBamFiles-Picard 2020-01-07T20:49:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897072-CalculateFingerprintMetrics-Picard 2020-01-07T20:43:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897092-PathSeqBuildReferenceTaxonomy 2023-11-09T16:17:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897112-CompareBaseQualities 2020-01-07T20:44:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897132-CollectSequencingArtifactMetrics-Picard 2020-01-07T20:44:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897152-MappedReadFilter 2020-01-07T20:50:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897172-MarkDuplicatesWithMateCigar-Picard 2020-01-07T20:50:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897192-CpxVariantReInterpreterSpark-BETA 2020-01-07T20:48:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897212-IntervalListTools-Picard 2020-01-07T20:49:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897232-CollectInsertSizeMetrics-Picard 2020-01-07T20:44:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897252-SortSamSpark-BETA 2020-01-07T20:51:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897272-LeftAlignIndels 2020-01-07T20:49:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897292-MappingQualityNotZeroReadFilter 2020-01-07T20:50:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897312-MateDifferentStrandReadFilter 2020-01-07T20:50:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897332-NonNFastaSize-Picard 2020-01-07T20:50:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897352-FilterMutectCalls 2020-01-07T20:49:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897372-BaseRecalibratorSpark-BETA 2020-01-07T20:43:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897392-CalculateMixingFractions 2020-01-07T20:43:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897412-SelectVariants 2020-01-07T20:51:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897432-ReadGroupReadFilter 2020-01-07T20:50:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897452-GenomicsDBImport 2020-01-07T20:49:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897472-CollectQualityYieldMetricsSpark-BETA 2020-01-07T20:44:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897492-PlatformUnitReadFilter 2020-01-07T20:50:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897512-PrintReads 2020-01-07T20:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897532-HaplotypeCaller 2020-01-07T20:49:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897552-ReadsPipelineSpark-BETA 2020-11-17T19:16:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897572-ReplaceSamHeader-Picard 2020-01-07T20:51:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897592-CountFalsePositives-BETA 2020-01-07T20:48:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897612-MateUnmappedAndUnmappedReadFilter 2020-01-07T20:50:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897632-CollectIlluminaLaneMetrics-Picard 2020-01-07T20:44:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897652-PolymorphicNuMT 2020-01-07T20:50:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897672-VcfToIntervalList-Picard 2020-01-07T20:51:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897692-MarkDuplicatesGATK-EXPERIMENTAL 2020-01-07T20:50:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897712-SetNmAndUqTags-Picard 2020-01-07T20:51:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897732-MarkIlluminaAdapters-Picard 2020-01-07T20:50:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897772-MatchingBasesAndQualsReadFilter 2020-01-07T20:50:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897792-MeanQualityByCycleSpark-BETA 2020-01-07T20:50:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897812-CollectTargetedPcrMetrics-Picard 2020-01-07T20:44:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897832-CollectBaseDistributionByCycle-Picard 2020-01-07T20:44:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897852-ReblockGVCF-EXPERIMENTAL 2020-01-07T20:51:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897872-MergeBamAlignment-Picard 2021-07-14T19:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897892-LeftAlignAndTrimVariants 2020-01-07T20:49:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897912-ModelSegments-BETA 2020-01-07T20:50:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897952-RevertSamSpark-BETA 2020-01-07T20:51:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897972-ExtractIlluminaBarcodes-Picard 2020-01-07T20:49:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036897992-BedToIntervalList-Picard 2020-01-07T20:43:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898012-RemoveNearbyIndels 2020-01-07T20:51:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898032-MarkDuplicates-Picard 2020-01-07T20:50:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898052-CreateSequenceDictionary-Picard 2020-01-07T20:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898112-GenotypeSummaries 2020-01-07T20:49:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898172-PairedReadFilter 2020-01-07T20:50:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898192-GetPileupSummaries-BETA 2020-01-07T20:49:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898232-FifoBuffer-Picard 2020-01-07T20:49:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898252-ExcessHet 2020-01-07T20:49:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898272-LikelihoodRankSumTest 2020-01-07T20:50:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898312-BaseRecalibrator 2023-11-28T00:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898352-RevertBaseQualityScores 2020-01-07T20:51:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898412-EstimateLibraryComplexityGATK-BETA 2020-01-07T20:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898452-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T20:51:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898492-CollectInsertSizeMetricsSpark-BETA 2020-01-07T20:44:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898512-BaseQualityRankSumTest 2020-01-07T20:43:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898572-ApplyVQSR 2020-01-07T20:43:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898612-GermlineCNVCaller-BETA 2020-01-07T20:49:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898632-ReadNameReadFilter 2020-01-07T20:50:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898652-MappingQualityZero 2020-01-07T20:50:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898672-CallCopyRatioSegments-BETA 2020-01-07T20:43:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898692-ScatterIntervalsByNs-Picard 2020-01-07T20:51:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898712-AS-InbreedingCoeff 2020-01-07T20:43:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898732-BamIndexStats-Picard 2020-01-07T20:43:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898772-VcfFormatConverter-Picard 2020-01-07T20:51:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898792-CombineGVCFs 2020-01-07T20:44:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898812-CollectGcBiasMetrics-Picard 2020-01-07T20:44:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898832-AddOATag-Picard 2020-01-07T20:43:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898852-ReadPosition 2020-01-07T20:50:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898872-ReadStrandFilter 2020-01-07T20:51:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898892-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-01-07T20:48:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898912-CalculateGenotypePosteriors 2020-01-07T20:43:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898932-MergeVcfs-Picard 2020-01-07T20:50:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898952-CollectMultipleMetrics-Picard 2020-01-07T20:44:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898972-ValidateVariants 2020-01-07T20:51:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360036898992-CollectAllelicCounts-BETA 2020-01-07T20:44:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899052-CombineSegmentBreakpoints-EXPERIMENTAL 2020-01-07T20:44:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899072-BaitDesigner-Picard 2020-01-07T20:43:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899092-FixMateInformation-Picard 2020-01-07T20:49:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899112-SortVcf-Picard 2020-01-07T20:51:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899152-FastqToSam-Picard 2020-01-07T20:49:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899192-SamToFastq-Picard 2020-01-07T20:51:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899212-CollectIlluminaBasecallingMetrics-Picard 2020-01-07T20:44:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899252-FuncotatorDataSourceDownloader-BETA 2020-01-07T20:49:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899272-StrandArtifact 2020-01-07T20:51:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899292-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-01-07T20:44:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899312-GatherVcfsCloud-BETA 2020-01-07T20:49:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899372-AS-MappingQualityRankSumTest 2020-01-07T20:43:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899412-CollectFragmentCounts-BETA 2021-07-16T09:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899452-BaseQuality 2020-01-07T20:43:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899492-SeqIsStoredReadFilter 2020-01-07T20:51:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899512-CollectBaseDistributionByCycleSpark-BETA 2020-01-07T20:44:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899532-VariantRecalibrator 2020-01-07T20:51:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899552-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-01-07T20:49:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899572-PlotDenoisedCopyRatios-BETA 2020-01-07T20:50:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899592-SplitIntervals 2020-01-07T20:51:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899612-FastaAlternateReferenceMaker 2020-01-07T20:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899632-StructuralVariationDiscoveryPipelineSpark-BETA 2020-01-07T20:51:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899652-SplitNCigarReads 2020-01-07T20:51:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899672-ProperlyPairedReadFilter 2020-01-07T20:50:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899692-CigarContainsNoNOperator 2020-01-07T20:43:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899712-CNNVariantTrain-EXPERIMENTAL 2020-01-07T20:43:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899732-GenotypeGVCFs 2020-01-07T20:49:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899752-TandemRepeat 2020-01-07T20:51:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899772-FindBadGenomicKmersSpark-BETA 2020-01-07T20:49:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899792-AddCommentsToBam-Picard 2020-01-07T20:43:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899812-AS-QualByDepth 2020-01-07T20:43:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899832-Concordance-BETA 2020-01-07T20:44:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899852-BuildBamIndex-Picard 2020-01-07T20:43:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899872-NotSecondaryAlignmentReadFilter 2020-01-07T20:50:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899892-IndexFeatureFile 2024-01-30T22:11:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899912-ValidAlignmentEndReadFilter 2020-01-07T20:51:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899932-ConvertSequencingArtifactToOxoG-Picard 2020-01-07T20:44:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899952-OrientationBiasReadCounts 2020-01-07T20:50:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360036899972-CountNs 2020-01-07T20:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360036900012-CollectOxoGMetrics-Picard 2020-01-07T20:44:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360036900052-CountBasesSpark-BETA 2020-01-07T20:48:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360036900132-CreateSomaticPanelOfNormals-BETA 2020-01-07T20:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360036900172-CheckPileup 2020-01-07T20:43:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360036900212-CheckTerminatorBlock-Picard 2020-01-07T20:43:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051252-LibraryReadFilter 2020-01-07T20:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051272-NonChimericOriginalAlignmentReadFilter 2020-01-07T20:58:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051292-GenotypeConcordance-Picard 2020-01-07T20:58:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051312-OverclippedReadFilter 2020-01-07T20:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051332-Funcotator-BETA 2020-01-07T20:58:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051352-PathSeqPipelineSpark 2020-01-07T20:59:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051372-CalcMetadataSpark-BETA 2020-01-07T20:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051392-AS-StrandOddsRatio 2020-01-07T20:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051412-AnnotatePairOrientation-BETA 2020-01-07T20:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051432-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:00:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051452-EstimateLibraryComplexity-Picard 2020-01-07T20:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051472-AnnotateVcfWithExpectedAlleleFraction 2020-01-07T20:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051492-AllowAllReadsReadFilter 2020-01-07T20:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051512-NotDuplicateReadFilter 2020-01-07T20:59:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051532-BamToBfq-Picard 2020-01-07T20:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051552-VariantAnnotator-BETA 2020-01-07T21:00:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051572-CollectMultipleMetricsSpark-BETA 2020-01-07T20:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051592-StrandOddsRatio 2020-01-07T20:59:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051612--Tool-Documentation-Index 2020-01-07T20:56:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051632-HasReadGroupReadFilter 2020-01-07T20:58:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051652-UniqueAltReadCount 2020-01-07T21:00:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051672-VariantsToTable 2020-01-07T21:00:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051692-CNNVariantWriteTensors-EXPERIMENTAL 2020-01-07T20:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051712-CountVariantsSpark-BETA 2020-01-07T20:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051732-UpdateVCFSequenceDictionary 2020-01-07T21:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051752-IlluminaBasecallsToFastq-Picard 2020-01-07T20:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051772-SoftClippedReadFilter 2020-01-07T20:59:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051832-GetSampleName-BETA 2020-01-07T20:58:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051852-CalculateReadGroupChecksum-Picard 2020-01-07T20:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051872-SortReadFileSpark-BETA 2020-01-07T20:59:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051892-GatherBamFiles-Picard 2020-01-07T20:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051912-PathSeqBuildReferenceTaxonomy 2020-01-07T20:59:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051932-MappedReadFilter 2020-01-07T20:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051952-GatherBQSRReports 2020-01-07T20:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051972-CalculateContamination 2020-01-07T20:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037051992-ApplyBQSR 2020-01-07T20:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052012-CpxVariantReInterpreterSpark-BETA 2020-01-07T20:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052032-PathSeqBuildKmers 2020-01-07T20:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052052-IntervalListTools-Picard 2020-01-07T20:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052092-StrandBiasBySample 2020-01-07T20:59:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052112-CollectReadCounts-BETA 2020-01-07T20:57:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052132-SortSamSpark-BETA 2020-01-07T20:59:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052172-FilterIntervals-BETA 2020-01-07T20:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052192-CollectJumpingLibraryMetrics-Picard 2020-01-07T20:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052212-SplitSamByNumberOfReads-Picard 2020-01-07T20:59:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052232-MateDifferentStrandReadFilter 2020-01-07T20:58:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052252-CalculateMixingFractions 2020-01-07T20:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052272-SelectVariants 2020-01-07T20:59:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052292-AccumulateVariantCallingMetrics-Picard 2020-01-07T20:56:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052312-IlluminaBasecallsToSam-Picard 2020-01-07T20:58:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052332-ReadGroupReadFilter 2020-01-07T20:59:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052352-MappingQualityReadFilter 2020-01-07T20:58:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052372-GenomicsDBImport 2020-01-07T20:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052392-CreateHadoopBamSplittingIndex-BETA 2020-01-07T20:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052412-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-01-07T20:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052432-CrosscheckReadGroupFingerprints-Picard 2020-01-07T20:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052452-ValidAlignmentStartReadFilter 2020-01-07T21:00:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052472-CountFalsePositives-BETA 2020-01-07T20:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052492-PolymorphicNuMT 2020-01-07T20:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052512-SetNmAndUqTags-Picard 2020-01-07T20:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052532-MatchingBasesAndQualsReadFilter 2020-01-07T20:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052572-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-01-07T20:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052592-MeanQualityByCycleSpark-BETA 2020-01-07T20:58:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052612-CollectBaseDistributionByCycle-Picard 2020-01-07T20:56:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052632-ReblockGVCF-EXPERIMENTAL 2020-01-07T20:59:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052652-FixMisencodedBaseQualityReads 2020-01-07T20:58:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052672-ModelSegments-BETA 2020-01-07T20:58:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052692-RevertSamSpark-BETA 2020-01-07T20:59:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052732-ExtractIlluminaBarcodes-Picard 2020-01-07T20:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052752-BedToIntervalList-Picard 2020-01-07T20:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052772-CollectRawWgsMetrics-Picard 2020-01-07T20:57:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052792-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-01-07T21:00:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard 2024-05-22T03:31:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052832-PositionBasedDownsampleSam-Picard 2020-01-07T20:59:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052852-ReorderSam-Picard 2020-01-07T20:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052872-FilterAlignmentArtifacts-EXPERIMENTAL 2020-01-07T20:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052892-PairedReadFilter 2020-01-07T20:59:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052912-AS-ReadPosRankSumTest 2020-01-07T20:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052932-GetPileupSummaries-BETA 2020-01-07T20:58:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052952-VariantFiltration 2020-01-07T21:00:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052972-BaseRecalibrator 2020-01-07T20:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037052992-RevertBaseQualityScores 2020-01-07T20:59:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053012-GatherTranches-BETA 2020-01-07T20:58:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053032-ClippingRankSumTest 2020-01-07T20:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053052-BQSRPipelineSpark-BETA 2020-01-07T20:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053072-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:00:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053092-PossibleDeNovo 2020-01-07T20:59:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053112-CollectInsertSizeMetricsSpark-BETA 2020-01-07T20:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053132-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:00:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053152-UpdateVcfSequenceDictionary-Picard 2020-01-07T21:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053172-MappingQualityZero 2020-01-07T20:58:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053192-AS-InbreedingCoeff 2020-01-07T20:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053212-FilterMutectCalls-BETA 2020-01-07T20:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053232-Mutect2-BETA 2020-01-07T20:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053252-CollectVariantCallingMetrics-Picard 2020-01-07T20:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053272-CombineGVCFs 2020-01-07T20:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053292-CollectGcBiasMetrics-Picard 2020-01-07T20:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053312-AddOATag-Picard 2020-01-07T20:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053332-Coverage 2020-01-07T20:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053352-ReadStrandFilter 2020-01-07T20:59:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053372-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-01-07T20:57:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053392-MergeVcfs-Picard 2020-01-07T20:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053412-CollectAllelicCounts-BETA 2020-01-07T20:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053432-MethylationTypeCaller-EXPERIMENTAL 2020-01-07T20:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053452-PreprocessIntervals-BETA 2020-01-07T20:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053472-QualityScoreDistribution-Picard 2020-01-07T20:59:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053492-ReadLengthEqualsCigarLengthReadFilter 2020-01-07T20:59:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053512-FixMateInformation-Picard 2020-01-07T20:58:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053532-ReadGroupBlackListReadFilter 2020-01-07T20:59:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053552-MergeSamFiles-Picard 2020-01-07T20:58:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053572-GatherVcfsCloud-BETA 2020-01-07T20:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053592-AnnotateIntervals-BETA 2020-01-07T20:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053612-PathSeqScoreSpark 2020-01-07T20:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053632-RevertSam-Picard 2020-01-07T20:59:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053652-SplitReads 2020-01-07T20:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053672-BaseRecalibratorSparkSharded-EXPERIMENTAL 2020-01-07T20:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053692-ReadPosRankSumTest 2020-01-07T20:59:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053712-IntervalOverlapReadFilter 2020-01-07T20:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053732-NonZeroReferenceLengthAlignmentReadFilter 2020-01-07T20:58:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053752-CollectBaseDistributionByCycleSpark-BETA 2020-01-07T20:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053772-VariantRecalibrator 2020-01-07T21:00:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053792-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-01-07T20:57:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053812-SplitIntervals 2020-01-07T20:59:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053832-UnmarkDuplicates 2020-01-07T21:00:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053852-SplitNCigarReads 2020-01-07T20:59:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053872-NonZeroFragmentLengthReadFilter 2020-01-07T20:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053892-PileupSpark-BETA 2020-01-07T20:59:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053912-ProperlyPairedReadFilter 2020-01-07T20:59:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053932-CNNVariantTrain-EXPERIMENTAL 2020-01-07T20:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053952-TandemRepeat 2020-01-07T21:00:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053972-AddCommentsToBam-Picard 2020-01-07T20:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037053992-AnalyzeSaturationMutagenesis-BETA 2020-01-07T20:56:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054012-AS-BaseQualityRankSumTest 2020-01-07T20:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054032-BuildBamIndex-Picard 2020-01-07T20:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054052-NotSecondaryAlignmentReadFilter 2020-01-07T20:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054092-FindMendelianViolations-Picard 2020-01-07T20:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054112-ReferenceBases 2020-01-07T20:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054132-IndexFeatureFile 2020-01-07T20:58:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054152-MetricsReadFilter 2020-01-07T20:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054172-FastaReferenceMaker 2020-01-07T20:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054192-QualityScoreDistributionSpark-BETA 2020-01-07T20:59:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054212-ConvertSequencingArtifactToOxoG-Picard 2020-01-07T20:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054232-OrientationBiasReadCounts 2020-01-07T20:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054252-CollectOxoGMetrics-Picard 2020-01-07T20:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054272-CreateReadCountPanelOfNormals-BETA 2020-01-07T20:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054292-CountBasesSpark-BETA 2020-01-07T20:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054312-ASEReadCounter 2020-01-07T20:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054332-FilterVariantTranches-EXPERIMENTAL 2020-01-07T20:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054372-ReadLengthReadFilter 2020-01-07T20:59:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054732-ChromosomeCounts 2020-01-07T21:01:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054752-LibraryReadFilter 2020-01-07T21:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054772-Pileup 2020-01-07T21:03:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054792-OverclippedReadFilter 2020-01-07T21:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054812-BwaMemIndexImageCreator 2023-11-10T19:15:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054832-Funcotator-BETA 2020-01-07T21:02:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054852-CollectQualityYieldMetrics-Picard 2020-01-07T21:01:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054872-PathSeqPipelineSpark 2020-01-07T21:03:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054892-SecondOfPairReadFilter 2020-01-07T21:03:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054912-AS-StrandOddsRatio 2020-01-07T21:00:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054932-FilterVcf-Picard 2020-01-07T21:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054952-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-01-07T21:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054972-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037054992-CountReads 2020-01-07T21:01:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055012-CollectHsMetrics-Picard 2020-01-07T21:01:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055032-CountVariants 2020-01-07T21:01:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055052-AllowAllReadsReadFilter 2020-01-07T21:00:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055072-LiftOverIntervalList-Picard 2020-01-07T21:02:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055092-NotDuplicateReadFilter 2020-01-07T21:03:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055112-BamToBfq-Picard 2020-01-07T21:00:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055132-VariantAnnotator-BETA 2020-01-07T21:04:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055152-PrimaryLineReadFilter 2020-01-07T21:03:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055172-CollectMultipleMetricsSpark-BETA 2020-01-07T21:01:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055192-CountBases 2020-01-07T21:01:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055212-CheckFingerprint-Picard 2020-01-07T21:00:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055232-UniqueAltReadCount 2020-01-07T21:04:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055272-VariantsToTable 2020-01-07T21:04:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055292-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:02:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055312-AS-RMSMappingQuality 2020-01-07T21:00:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055332-IlluminaBasecallsToFastq-Picard 2020-01-07T21:02:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055352-FisherStrand 2020-01-07T21:02:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055372-ClusterCrosscheckMetrics-Picard 2020-01-07T21:01:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055412-GetSampleName-BETA 2020-01-07T21:02:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055432-MarkDuplicatesSpark-BETA 2020-01-07T21:02:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055452-DepthPerAlleleBySample 2020-01-07T21:01:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055472-CalculateReadGroupChecksum-Picard 2020-01-07T21:00:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055492-CompareMetrics-Picard 2020-01-07T21:01:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055512-GatherBamFiles-Picard 2020-01-07T21:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055532-CalculateFingerprintMetrics-Picard 2020-01-07T21:00:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055552-PathSeqBuildReferenceTaxonomy 2020-01-07T21:03:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055572-AS-FisherStrand 2020-01-07T21:00:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055592-CompareBaseQualities 2020-01-07T21:01:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055612-AnnotateVcfWithBamDepth 2020-01-07T21:00:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055632-CollectSequencingArtifactMetrics-Picard 2020-01-07T21:01:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055652-MappedReadFilter 2020-01-07T21:02:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055672-ExtractSequences-Picard 2020-01-07T21:01:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055692-MarkDuplicatesWithMateCigar-Picard 2020-01-07T21:02:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055712-ApplyBQSR 2021-02-09T22:49:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055732-CpxVariantReInterpreterSpark-BETA 2020-01-07T21:01:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055752-IntervalListTools-Picard 2020-01-07T21:02:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055772-CollectInsertSizeMetrics-Picard 2024-03-15T07:29:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055792-CollectReadCounts-BETA 2020-01-07T21:01:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055812-LeftAlignIndels 2020-01-07T21:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055832-MappingQualityNotZeroReadFilter 2020-01-07T21:02:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055852-CollectJumpingLibraryMetrics-Picard 2020-01-07T21:01:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055872-MateDifferentStrandReadFilter 2020-01-07T21:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055892-NonNFastaSize-Picard 2020-01-07T21:03:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055912-FilterMutectCalls 2020-01-07T21:02:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055932-CalculateMixingFractions 2020-01-07T21:00:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants 2025-12-19T20:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055972-AccumulateVariantCallingMetrics-Picard 2020-01-07T21:00:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037055992-ReadGroupReadFilter 2020-01-07T21:03:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056012-GenomicsDBImport 2020-01-07T21:02:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056032-CollectQualityYieldMetricsSpark-BETA 2020-01-07T21:01:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056052-CrosscheckReadGroupFingerprints-Picard 2020-01-07T21:01:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056072-HaplotypeCaller 2020-01-07T21:02:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056092-ValidAlignmentStartReadFilter 2020-01-07T21:04:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056112-ReplaceSamHeader-Picard 2020-01-07T21:03:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056132-CountFalsePositives-BETA 2020-01-07T21:01:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056152-CountBasesInReference 2020-01-07T21:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056172-VcfToIntervalList-Picard 2020-01-07T21:04:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056192-SetNmAndUqTags-Picard 2020-01-07T21:03:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056212-PathSeqBwaSpark 2020-01-07T21:03:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056232-SampleList 2020-01-07T21:03:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056252-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-01-07T21:01:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056272-MeanQualityByCycleSpark-BETA 2020-01-07T21:02:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056292-FragmentLength 2020-01-07T21:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056312-CheckIlluminaDirectory-Picard 2020-01-07T21:00:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056332-CollectTargetedPcrMetrics-Picard 2020-01-07T21:01:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056352-CollectBaseDistributionByCycle-Picard 2020-01-07T21:01:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056372-ReblockGVCF-EXPERIMENTAL 2020-01-07T21:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056392-MergeBamAlignment-Picard 2020-01-07T21:03:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056412-FixMisencodedBaseQualityReads 2020-01-07T21:02:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056432-LeftAlignAndTrimVariants 2020-01-07T21:02:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056452-ModelSegments-BETA 2020-01-07T21:03:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056472-BedToIntervalList-Picard 2020-01-07T21:00:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056492-CollectRawWgsMetrics-Picard 2020-01-07T21:01:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056512-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-01-07T21:04:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056532-MarkDuplicates-Picard 2020-01-07T21:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056552-CreateSequenceDictionary-Picard 2020-01-07T21:01:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056572-VcfToAdpc-Picard 2020-01-07T21:04:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056592-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056612-PositionBasedDownsampleSam-Picard 2020-01-07T21:03:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056632-PostprocessGermlineCNVCalls-BETA 2020-01-07T21:03:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056652-NotSupplementaryAlignmentReadFilter 2020-01-07T21:03:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056672-GenotypeSummaries 2020-01-07T21:02:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056692-FlagStatSpark-BETA 2020-01-07T21:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056712-FilterAlignmentArtifacts-EXPERIMENTAL 2020-01-07T21:02:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056732-LikelihoodRankSumTest 2020-01-07T21:02:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056752-RevertBaseQualityScores 2020-01-07T21:03:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056772-GatherTranches-BETA 2020-01-07T21:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056792-DownsampleSam-Picard 2023-10-27T02:52:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056832-CompareSAMs-Picard 2020-01-07T21:01:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056852-EstimateLibraryComplexityGATK-BETA 2020-01-07T21:01:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056872-BaseQualityRankSumTest 2020-01-07T21:00:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056892-IntervalListToBed-Picard 2020-01-07T21:02:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056912-ApplyVQSR 2020-01-07T21:00:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056932-UpdateVcfSequenceDictionary-Picard 2020-01-07T21:04:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056952-ReadNameReadFilter 2020-01-07T21:03:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056972-MappingQualityZero 2020-01-07T21:02:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037056992-ScatterIntervalsByNs-Picard 2020-01-07T21:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057012-AS-InbreedingCoeff 2020-01-07T21:00:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057032-BamIndexStats-Picard 2020-01-07T21:00:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057052-FilterMutectCalls-BETA 2020-01-07T21:02:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057072-Mutect2-BETA 2020-01-07T21:03:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057092-VcfFormatConverter-Picard 2020-01-07T21:04:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057112-AddOrReplaceReadGroups-Picard 2020-01-07T21:00:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057132-CollectVariantCallingMetrics-Picard 2024-03-01T18:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057152-LiftoverVcf-Picard 2020-01-07T21:02:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057172-AddOATag-Picard 2020-01-07T21:00:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057192-Coverage 2020-01-07T21:01:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057212-ApplyBQSRSpark-BETA 2020-01-07T21:00:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057232-CollectMultipleMetrics-Picard 2020-01-07T21:01:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057272-ValidateVariants 2020-08-17T20:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057292-ExtractSVEvidenceSpark-BETA 2020-01-07T21:01:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057312-QualityScoreDistribution-Picard 2020-01-07T21:03:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057332-CombineSegmentBreakpoints-EXPERIMENTAL 2020-01-07T21:01:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057352-InbreedingCoeff 2020-01-07T21:02:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057372-FixMateInformation-Picard 2020-01-07T21:02:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057392-SortVcf-Picard 2020-01-07T21:04:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057412-FastqToSam-Picard 2020-01-07T21:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057432-ReadGroupBlackListReadFilter 2020-01-07T21:03:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057452-SortSam-Picard 2020-01-07T21:03:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057472-FuncotatorDataSourceDownloader-BETA 2020-01-07T21:02:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard 2020-01-07T21:01:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057512-PathSeqScoreSpark 2020-01-07T21:03:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057532-RevertSam-Picard 2020-01-07T21:03:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057552-FixCallSetSampleOrdering-EXPERIMENTAL 2020-01-07T21:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057572-BaseQuality 2020-01-07T21:00:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057592-NonZeroReferenceLengthAlignmentReadFilter 2020-01-07T21:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057612-CollectBaseDistributionByCycleSpark-BETA 2020-01-07T21:01:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057632-PathSeqFilterSpark 2020-01-07T21:03:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057652-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-01-07T21:01:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057672-PlotDenoisedCopyRatios-BETA 2020-01-07T21:03:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057692-FastaAlternateReferenceMaker 2020-01-07T21:01:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057712-StructuralVariationDiscoveryPipelineSpark-BETA 2020-01-07T21:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057732-EvaluateInfoFieldConcordance-BETA 2020-01-07T21:01:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057752-SplitNCigarReads 2020-01-07T21:04:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057772-PileupSpark-BETA 2020-01-07T21:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057792-FilterFuncotations-EXPERIMENTAL 2020-01-07T21:02:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057812-SplitSamByLibrary-Picard 2020-01-07T21:04:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057832-CrosscheckFingerprints-Picard 2020-01-07T21:01:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057852-GenotypeGVCFs 2023-06-13T13:35:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057872-FindBadGenomicKmersSpark-BETA 2020-01-07T21:02:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057892-AnalyzeSaturationMutagenesis-BETA 2020-01-07T21:00:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057912-AS-QualByDepth 2020-01-07T21:00:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057932-BuildBamIndex-Picard 2020-01-07T21:00:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057952-CollectRrbsMetrics-Picard 2020-01-07T21:01:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057972-NotSecondaryAlignmentReadFilter 2020-01-07T21:03:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037057992-ReferenceBases 2020-01-07T21:03:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058012-ValidAlignmentEndReadFilter 2020-01-07T21:04:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058032-FastaReferenceMaker 2020-01-07T21:01:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058052-DepthPerSampleHC 2020-01-07T21:01:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058072-AlleleFraction 2020-01-07T21:00:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058092-ConvertSequencingArtifactToOxoG-Picard 2020-01-07T21:01:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058112-RenameSampleInVcf-Picard 2020-01-07T21:03:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058132-CreateReadCountPanelOfNormals-BETA 2020-01-07T21:01:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058152-CountReadsSpark-BETA 2020-01-07T21:01:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058172-CreateSomaticPanelOfNormals-BETA 2023-10-23T06:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058192-CheckPileup 2020-01-07T21:00:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058212-GtcToVcf-Picard 2020-01-07T21:02:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058232-CheckTerminatorBlock-Picard 2020-01-07T21:01:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058472-MeanQualityByCycle-Picard 2020-01-07T21:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058492-GenotypeConcordance-Picard 2020-01-07T21:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058512-Pileup 2020-01-07T21:07:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058532-OverclippedReadFilter 2020-01-07T21:07:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058552-BwaMemIndexImageCreator 2020-01-07T21:05:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058572-WellformedReadFilter 2020-01-07T21:08:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058592-SampleReadFilter 2020-01-07T21:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058612-RMSMappingQuality 2020-01-07T21:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058632-CalcMetadataSpark-BETA 2020-01-07T21:05:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058652-SecondOfPairReadFilter 2020-01-07T21:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058672-AlignmentAgreesWithHeaderReadFilter 2020-01-07T21:04:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058692-FilterVcf-Picard 2020-01-07T21:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058712-AnnotatePairOrientation-BETA 2020-01-07T21:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058732-VariantEval-BETA 2020-01-07T21:08:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058752-GnarlyGenotyper-BETA 2020-01-07T21:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058772-ViewSam-Picard 2020-01-07T21:08:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058792-CountVariants 2020-01-07T21:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058812-AllowAllReadsReadFilter 2020-01-07T21:04:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058832-LiftOverIntervalList-Picard 2020-01-07T21:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058852-FilterSamReads-Picard 2020-01-07T21:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058872-CollectMultipleMetricsSpark-BETA 2020-01-07T21:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058892-DetermineGermlineContigPloidy-BETA 2020-01-07T21:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058912-QualByDepth 2020-01-07T21:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058932-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:06:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058952-AS-RMSMappingQuality 2020-01-07T21:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058972-CountVariantsSpark-BETA 2020-01-07T21:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037058992-SamFormatConverter-Picard 2020-01-07T21:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059012-FisherStrand 2020-01-07T21:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059052-ClusterCrosscheckMetrics-Picard 2020-01-07T21:05:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059072-GetSampleName-BETA 2020-01-07T21:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059112-DepthPerAlleleBySample 2020-01-07T21:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059132-SortReadFileSpark-BETA 2020-01-07T21:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059152-CompareMetrics-Picard 2020-01-07T21:05:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059172-FuncotateSegments-BETA 2020-01-07T21:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059192-GatherBamFiles-Picard 2020-01-07T21:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059212-PathSeqBuildReferenceTaxonomy 2020-01-07T21:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059232-BwaSpark-BETA 2020-01-07T21:05:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059252-CollectAlignmentSummaryMetrics-Picard 2020-01-07T21:05:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059272-GatherVcfs-Picard 2020-01-07T21:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059292-ExtractSequences-Picard 2020-01-07T21:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059312-CalculateContamination 2020-01-07T21:05:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059332-ApplyBQSR 2020-01-07T21:04:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059352-MakeSitesOnlyVcf-Picard 2020-01-07T21:07:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059372-IntervalListTools-Picard 2020-01-07T21:07:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059392-StrandBiasBySample 2020-01-07T21:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059412-CollectReadCounts-BETA 2020-01-07T21:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059432-FilterIntervals-BETA 2020-01-07T21:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059452-MappingQualityRankSumTest 2020-01-07T21:07:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059472-MappingQualityNotZeroReadFilter 2020-01-07T21:07:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059492-HaplotypeCallerSpark-BETA 2020-01-07T21:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059512-CollectJumpingLibraryMetrics-Picard 2020-01-07T21:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059532-SplitSamByNumberOfReads-Picard 2020-01-07T21:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059552-CalculateMixingFractions 2020-01-07T21:05:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059572-AccumulateVariantCallingMetrics-Picard 2020-01-07T21:04:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059592-ReadGroupReadFilter 2020-01-07T21:08:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059612-MappingQualityReadFilter 2020-01-07T21:07:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059632-GenomicsDBImport 2020-01-07T21:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059652-PlatformUnitReadFilter 2020-01-07T21:07:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059672-OxoGReadCounts 2020-01-07T21:07:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059692-CreateHadoopBamSplittingIndex-BETA 2020-01-07T21:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059712-CrosscheckReadGroupFingerprints-Picard 2020-01-07T21:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059732-HaplotypeCaller 2020-12-08T06:47:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059752-ValidAlignmentStartReadFilter 2020-01-07T21:08:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059792-ReadsPipelineSpark-BETA 2020-01-07T21:08:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059812-ReplaceSamHeader-Picard 2020-01-07T21:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059832-CountFalsePositives-BETA 2020-01-07T21:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059872-PolymorphicNuMT 2020-01-07T21:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059892-MarkDuplicatesGATK-EXPERIMENTAL 2020-01-07T21:07:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059932-PathSeqBwaSpark 2020-01-07T21:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059952-MarkIlluminaAdapters-Picard 2020-01-07T21:07:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059972-SampleList 2020-01-07T21:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037059992-MatchingBasesAndQualsReadFilter 2020-01-07T21:07:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060012-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-01-07T21:06:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060032-FragmentLength 2020-01-07T21:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060052-CollectBaseDistributionByCycle-Picard 2020-01-07T21:05:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060072-MergeBamAlignment-Picard 2020-01-07T21:07:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060112-LeftAlignAndTrimVariants 2020-01-07T21:07:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060132-ModelSegments-BETA 2020-01-07T21:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060152-RevertSamSpark-BETA 2020-01-07T21:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060172-ExtractIlluminaBarcodes-Picard 2020-01-07T21:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060192-BedToIntervalList-Picard 2020-01-07T21:04:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060212-RemoveNearbyIndels 2020-01-07T21:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060232-FilterByOrientationBias-EXPERIMENTAL 2020-01-07T21:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060252-OriginalAlignment 2020-01-07T21:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060272-MarkDuplicates-Picard 2020-01-07T21:07:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060312-CreateSequenceDictionary-Picard 2020-01-07T21:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060332-VcfToAdpc-Picard 2020-01-07T21:08:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060352-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:06:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060372-ReorderSam-Picard 2020-01-07T21:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060392-PostprocessGermlineCNVCalls-BETA 2020-01-07T21:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060412-NotSupplementaryAlignmentReadFilter 2020-01-07T21:07:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060432-GenotypeSummaries 2020-01-07T21:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060452-FilterAlignmentArtifacts-EXPERIMENTAL 2020-01-07T21:06:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060472-PairedReadFilter 2020-01-07T21:07:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060492-GetPileupSummaries-BETA 2020-01-07T21:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060512-ExcessHet 2020-01-07T21:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060532-LikelihoodRankSumTest 2020-01-07T21:07:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060552-DownsampleSam-Picard 2020-01-07T21:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060572-ClippingRankSumTest 2020-01-07T21:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060592-CompareSAMs-Picard 2020-01-07T21:05:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060612-BQSRPipelineSpark-BETA 2020-01-07T21:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060632-EstimateLibraryComplexityGATK-BETA 2020-01-07T21:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060652-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:08:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060672-CollectInsertSizeMetricsSpark-BETA 2020-01-07T21:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060692-BaseQualityRankSumTest 2020-01-07T21:04:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060812-CallCopyRatioSegments-BETA 2020-01-07T21:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060832-AS-InbreedingCoeff 2020-01-07T21:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060852-BamIndexStats-Picard 2020-01-07T21:04:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060872-FilterMutectCalls 2020-01-07T21:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060892-VcfFormatConverter-Picard 2020-01-07T21:08:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060912-CollectVariantCallingMetrics-Picard 2020-01-07T21:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard 2022-06-17T17:51:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060952-AddOATag-Picard 2020-01-07T21:04:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060972-Coverage 2020-01-07T21:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037060992-ReadStrandFilter 2020-01-07T21:08:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061012-ApplyBQSRSpark-BETA 2020-01-07T21:04:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061032-CollectMultipleMetrics-Picard 2020-01-07T21:05:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061052-CollectAllelicCounts-BETA 2020-01-07T21:05:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061072-CNNScoreVariants-EXPERIMENTAL 2020-01-07T21:05:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061092-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-01-07T21:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061112-MethylationTypeCaller-EXPERIMENTAL 2020-01-07T21:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061132-FlagStat 2020-01-07T21:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061152-InbreedingCoeff 2020-01-07T21:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061172-FixMateInformation-Picard 2020-01-07T21:06:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061192-ValidateSamFile-Picard 2020-01-07T21:08:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061212-ReadGroupBlackListReadFilter 2020-01-07T21:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061232-SortSam-Picard 2020-01-07T21:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061252-FuncotatorDataSourceDownloader-BETA 2020-01-07T21:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061272-StrandArtifact 2020-01-07T21:08:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061292-MergeSamFiles-Picard 2020-01-07T21:07:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061312-CollectRnaSeqMetrics-Picard 2020-01-07T21:05:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061332-PathSeqScoreSpark 2020-01-07T21:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061352-RevertSam-Picard 2020-01-07T21:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061372-PassesVendorQualityCheckReadFilter 2020-01-07T21:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061392-AS-MappingQualityRankSumTest 2020-01-07T21:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061412-CollectFragmentCounts-BETA 2020-01-07T21:05:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061432-BaseRecalibratorSparkSharded-EXPERIMENTAL 2020-01-07T21:04:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061452-SeqIsStoredReadFilter 2020-01-07T21:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061472-CollectBaseDistributionByCycleSpark-BETA 2020-01-07T21:05:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061492-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-01-07T21:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061512-FastaAlternateReferenceMaker 2020-01-07T21:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061532-StructuralVariationDiscoveryPipelineSpark-BETA 2020-01-07T21:08:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061552-EvaluateInfoFieldConcordance-BETA 2020-01-07T21:06:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061572-PileupSpark-BETA 2020-01-07T21:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061592-ProperlyPairedReadFilter 2020-01-07T21:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061612-FilterFuncotations-EXPERIMENTAL 2020-01-07T21:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061632-SplitSamByLibrary-Picard 2020-01-07T21:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061652-FindBadGenomicKmersSpark-BETA 2020-01-07T21:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061672-AnalyzeSaturationMutagenesis-BETA 2020-01-07T21:04:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061692-AS-QualByDepth 2020-01-07T21:04:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061712-AS-BaseQualityRankSumTest 2020-01-07T21:04:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061732-FragmentLengthReadFilter 2020-01-07T21:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061752-CollectRrbsMetrics-Picard 2020-01-07T21:05:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061772-NotSecondaryAlignmentReadFilter 2020-01-07T21:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061792-FindMendelianViolations-Picard 2020-01-07T21:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061812-ReferenceBases 2020-01-07T21:08:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061832-MetricsReadFilter 2020-01-07T21:07:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061852-FastaReferenceMaker 2020-01-07T21:06:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061872-QualityScoreDistributionSpark-BETA 2020-01-07T21:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061892-DepthPerSampleHC 2020-01-07T21:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061912-ConvertSequencingArtifactToOxoG-Picard 2020-01-07T21:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061932-OrientationBiasReadCounts 2020-01-07T21:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061952-CollectOxoGMetrics-Picard 2020-01-07T21:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061972-CountBasesSpark-BETA 2020-01-07T21:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037061992-PrintReadsSpark-BETA 2020-01-07T21:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037062012-CreateSomaticPanelOfNormals-BETA 2020-01-07T21:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037062032-CheckTerminatorBlock-Picard 2020-01-07T21:05:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037062052-ReadLengthReadFilter 2020-01-07T21:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037062072-CleanSam-Picard 2020-01-07T21:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063072-CollectIndependentReplicateMetrics-Picard-BETA 2020-01-07T21:09:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063092-LibraryReadFilter 2020-01-07T21:11:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063112-MeanQualityByCycle-Picard 2020-01-07T21:11:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063132-CollectHiSeqXPfFailMetrics-Picard 2020-01-07T21:09:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063152-OverclippedReadFilter 2020-01-07T21:11:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063172-BwaMemIndexImageCreator 2020-01-07T21:09:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063192-WellformedReadFilter 2020-01-07T21:13:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063212-SampleReadFilter 2020-01-07T21:12:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063232-AnalyzeCovariates 2020-01-07T21:09:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063252-FirstOfPairReadFilter 2020-01-07T21:10:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063272-CollectQualityYieldMetrics-Picard 2020-01-07T21:09:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063292-PathSeqPipelineSpark 2020-01-07T21:12:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063312-CalcMetadataSpark-BETA 2020-01-07T21:09:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063332-AlignmentAgreesWithHeaderReadFilter 2020-01-07T21:09:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063352-AS-StrandOddsRatio 2020-01-07T21:09:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063372-AnnotatePairOrientation-BETA 2020-01-07T21:09:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063392-VariantEval-BETA 2020-01-07T21:13:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063412-CountReads 2020-01-07T21:10:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063432-FixVcfHeader-Picard 2020-01-07T21:10:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063452-CollectHsMetrics-Picard 2020-01-07T21:09:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063472-GnarlyGenotyper-BETA 2020-01-07T21:11:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063492-EstimateLibraryComplexity-Picard 2020-01-07T21:10:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063512-ViewSam-Picard 2020-01-07T21:13:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063532-CountVariants 2020-01-07T21:10:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063552-AllowAllReadsReadFilter 2020-01-07T21:09:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063572-CountBases 2020-01-07T21:10:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063592-DetermineGermlineContigPloidy-BETA 2020-01-07T21:10:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063612-FindBreakpointEvidenceSpark-BETA 2020-01-07T21:10:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063632-MappingQuality 2020-01-07T21:11:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063652-QualByDepth 2020-01-07T21:12:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063672-VariantsToTable 2020-01-07T21:13:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063692-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:10:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063712-NormalizeFasta-Picard 2020-01-07T21:11:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063732-AS-RMSMappingQuality 2020-01-07T21:09:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063752-IlluminaBasecallsToFastq-Picard 2020-01-07T21:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063772-ClusterCrosscheckMetrics-Picard 2020-01-07T21:09:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063792-ClipReads 2020-01-07T21:09:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063812-SoftClippedReadFilter 2020-01-07T21:12:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063832-GetSampleName-BETA 2020-01-07T21:11:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063852-MarkDuplicatesSpark-BETA 2020-01-07T21:11:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063872-DepthPerAlleleBySample 2020-01-07T21:10:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063892-CalculateReadGroupChecksum-Picard 2020-01-07T21:09:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063912-FuncotateSegments-BETA 2020-01-07T21:11:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063932-GatherBamFiles-Picard 2020-01-07T21:11:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063952-CalculateFingerprintMetrics-Picard 2020-01-07T21:09:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063972-PathSeqBuildReferenceTaxonomy 2020-01-07T21:12:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037063992-CollectAlignmentSummaryMetrics-Picard 2020-01-07T21:09:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064012-AnnotateVcfWithBamDepth 2020-01-07T21:09:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064032-GatherVcfs-Picard 2020-01-07T21:11:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064052-MarkDuplicatesWithMateCigar-Picard 2020-01-07T21:11:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064072-ApplyBQSR 2020-01-07T21:09:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064092-PathSeqBuildKmers 2020-01-07T21:12:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064112-CollectInsertSizeMetrics-Picard 2020-01-07T21:09:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064132-CollectReadCounts-BETA 2020-01-07T21:10:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064152-LeftAlignIndels 2020-01-07T21:11:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064172-FilterIntervals-BETA 2020-01-07T21:10:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064192-MappingQualityNotZeroReadFilter 2020-01-07T21:11:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064232-SplitSamByNumberOfReads-Picard 2020-01-07T21:12:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064252-MateDifferentStrandReadFilter 2020-01-07T21:11:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064292-FilterMutectCalls 2020-01-07T21:10:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064312-BaseRecalibratorSpark-BETA 2020-01-07T21:09:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064332-AccumulateVariantCallingMetrics-Picard 2020-01-07T21:09:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064352-GenomicsDBImport 2020-01-07T21:11:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064372-CollectQualityYieldMetricsSpark-BETA 2020-01-07T21:09:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064392-CreateHadoopBamSplittingIndex-BETA 2020-01-07T21:10:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064412-PrintReads 2020-01-07T21:12:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064432-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-01-07T21:09:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064452-HaplotypeCaller 2020-01-07T21:11:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064472-ValidAlignmentStartReadFilter 2020-01-07T21:13:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064492-CountFalsePositives-BETA 2020-01-07T21:10:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064512-PolymorphicNuMT 2020-01-07T21:12:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064532-VcfToIntervalList-Picard 2020-01-07T21:13:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064552-MarkDuplicatesGATK-EXPERIMENTAL 2020-01-07T21:11:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064592-SampleList 2020-01-07T21:12:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064612-MatchingBasesAndQualsReadFilter 2020-01-07T21:11:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064632-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-01-07T21:10:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064652-FragmentLength 2020-01-07T21:11:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064672-CollectTargetedPcrMetrics-Picard 2020-01-07T21:10:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064692-ReblockGVCF-EXPERIMENTAL 2020-01-07T21:12:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064712-FixMisencodedBaseQualityReads 2020-01-07T21:10:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064732-LeftAlignAndTrimVariants 2020-01-07T21:11:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064752-ModelSegments-BETA 2020-01-07T21:11:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064772-RevertSamSpark-BETA 2020-01-07T21:12:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064792-ExtractIlluminaBarcodes-Picard 2020-01-07T21:10:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064812-AmbiguousBaseReadFilter 2020-01-07T21:09:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064832-BedToIntervalList-Picard 2020-01-07T21:09:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064852-CompareDuplicatesSpark-BETA 2020-01-07T21:10:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064872-CollectRawWgsMetrics-Picard 2020-01-07T21:09:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064892-FilterByOrientationBias-EXPERIMENTAL 2020-01-07T21:10:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064912-OriginalAlignment 2020-01-07T21:11:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064932-CreateSequenceDictionary-Picard 2020-01-07T21:10:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064952-VcfToAdpc-Picard 2020-01-07T21:13:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064972-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:10:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037064992-ReorderSam-Picard 2020-01-07T21:12:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065032-FlagStatSpark-BETA 2020-01-07T21:11:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065052-PairedReadFilter 2020-01-07T21:12:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065072-FifoBuffer-Picard 2020-01-07T21:10:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065092-BaseRecalibrator 2020-01-07T21:09:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065112-RevertBaseQualityScores 2020-01-07T21:12:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065132-GatherTranches-BETA 2020-01-07T21:11:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065152-DownsampleSam-Picard 2020-01-07T21:10:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065172-CompareSAMs-Picard 2020-01-07T21:10:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065192-BQSRPipelineSpark-BETA 2020-01-07T21:09:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065212-EstimateLibraryComplexityGATK-BETA 2020-01-07T21:10:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065232-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:12:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065252-PossibleDeNovo 2020-01-07T21:12:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065272-CollectInsertSizeMetricsSpark-BETA 2020-01-07T21:09:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065292-DenoiseReadCounts-BETA 2020-01-07T21:10:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065312-BaseQualityRankSumTest 2020-01-07T21:09:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065332-GermlineCNVCaller-BETA 2020-01-07T21:11:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065352-UpdateVcfSequenceDictionary-Picard 2020-01-07T21:13:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065372-ReadNameReadFilter 2020-01-07T21:12:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065392-MappingQualityZero 2020-01-07T21:11:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065412-ScatterIntervalsByNs-Picard 2020-01-07T21:12:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065432-AS-InbreedingCoeff 2020-01-07T21:09:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065452-FilterMutectCalls 2020-01-07T21:10:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065472-Mutect2 2020-01-07T21:11:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065492-CollectVariantCallingMetrics-Picard 2020-01-07T21:10:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065512-CollectGcBiasMetrics-Picard 2020-01-07T21:09:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065532-AddOATag-Picard 2020-01-07T21:09:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065552-ReadPosition 2020-01-07T21:12:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065572-MateOnSameContigOrNoMappedMateReadFilter 2020-01-07T21:11:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065592-Coverage 2020-01-07T21:10:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065612-CalculateGenotypePosteriors 2020-01-07T21:09:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065632-CollectMultipleMetrics-Picard 2020-01-07T21:09:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065652-ExtractSVEvidenceSpark-BETA 2020-01-07T21:10:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065672-CollectAllelicCounts-BETA 2020-01-07T21:09:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065692-MethylationTypeCaller-EXPERIMENTAL 2020-01-07T21:11:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065712-QualityScoreDistribution-Picard 2020-01-07T21:12:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065732-BaitDesigner-Picard 2020-01-07T21:09:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065752-PrintVariantsSpark-BETA 2020-01-07T21:12:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065772-ValidateSamFile-Picard 2020-01-07T21:13:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065792-FuncotatorDataSourceDownloader-BETA 2020-01-07T21:11:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065812-StrandArtifact 2020-01-07T21:12:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065832-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-01-07T21:10:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065852-CollectRnaSeqMetrics-Picard 2020-01-07T21:10:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065872-GatherVcfsCloud-BETA 2020-01-07T21:11:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065892-AnnotateIntervals-BETA 2020-01-07T21:09:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065912-PassesVendorQualityCheckReadFilter 2020-01-07T21:12:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065932-SplitReads 2020-01-07T21:12:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065952-CollectFragmentCounts-BETA 2020-01-07T21:09:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065972-BaseRecalibratorSparkSharded-EXPERIMENTAL 2020-01-07T21:09:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037065992-ReadPosRankSumTest 2020-01-07T21:12:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066032-CollectBaseDistributionByCycleSpark-BETA 2020-01-07T21:09:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066052-VariantRecalibrator 2020-01-07T21:13:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066072-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-01-07T21:10:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066092-SplitIntervals 2020-01-07T21:12:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066112-UnmarkDuplicates 2020-01-07T21:12:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066132-PileupSpark-BETA 2020-01-07T21:12:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066152-ProperlyPairedReadFilter 2020-01-07T21:12:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066172-SplitSamByLibrary-Picard 2020-01-07T21:12:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066192-CNNVariantTrain-EXPERIMENTAL 2020-01-07T21:09:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066212-FindBadGenomicKmersSpark-BETA 2020-01-07T21:10:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066232-Concordance-BETA 2020-01-07T21:10:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066252-FragmentLengthReadFilter 2020-01-07T21:11:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066272-CollectRrbsMetrics-Picard 2020-01-07T21:10:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066292-NotSecondaryAlignmentReadFilter 2020-01-07T21:11:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066312-IndexFeatureFile 2020-01-07T21:11:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066332-MetricsReadFilter 2020-01-07T21:11:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066352-FastaReferenceMaker 2020-01-07T21:10:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066372-QualityScoreDistributionSpark-BETA 2020-01-07T21:12:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066392-AlleleFraction 2020-01-07T21:09:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066412-ConvertSequencingArtifactToOxoG-Picard 2020-01-07T21:10:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066432-CountNs 2020-01-07T21:10:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066452-RenameSampleInVcf-Picard 2020-01-07T21:12:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066492-CollectOxoGMetrics-Picard 2020-01-07T21:09:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066512-PrintReadsSpark-BETA 2020-01-07T21:12:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066532-CreateSomaticPanelOfNormals-BETA 2020-01-07T21:10:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066552-GtcToVcf-Picard 2020-01-07T21:11:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066572-CheckTerminatorBlock-Picard 2020-01-07T21:09:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066592-ReadLengthReadFilter 2020-01-07T21:12:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066812-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2020-01-07T21:14:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066832-MeanQualityByCycle-Picard 2020-01-07T21:16:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066852-Pileup 2020-01-07T21:16:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066872-OverclippedReadFilter 2020-01-07T21:16:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066892-WellformedReadFilter 2020-01-07T21:17:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066912-AnalyzeCovariates 2020-01-07T21:13:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066932-RMSMappingQuality 2020-01-07T21:16:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066952-Funcotator-BETA 2020-01-07T21:15:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066972-CollectQualityYieldMetrics-Picard 2020-01-07T21:14:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037066992-AlignmentAgreesWithHeaderReadFilter 2020-01-07T21:13:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067012-AS-StrandOddsRatio 2020-01-07T21:13:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067032-FilterVcf-Picard 2020-01-07T21:15:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067052-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-01-07T21:16:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067072-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:17:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067092-FixVcfHeader-Picard 2020-01-07T21:15:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067112-CountVariants 2020-01-07T21:14:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067132-AllowAllReadsReadFilter 2020-01-07T21:13:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067152-LiftOverIntervalList-Picard 2020-01-07T21:15:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067172-NotDuplicateReadFilter 2020-01-07T21:16:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067192-BamToBfq-Picard 2020-01-07T21:13:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067212-FindBreakpointEvidenceSpark-BETA 2020-01-07T21:15:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067232-UniqueAltReadCount 2020-01-07T21:17:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067252-MappingQuality 2020-01-07T21:15:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067272-QualByDepth 2020-01-07T21:16:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067292-VariantsToTable 2020-01-07T21:17:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067312-NormalizeFasta-Picard 2020-01-07T21:16:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067332-CNNVariantWriteTensors-EXPERIMENTAL 2020-01-07T21:13:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067352-CountVariantsSpark-BETA 2020-01-07T21:14:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067372-UpdateVCFSequenceDictionary 2020-01-07T21:17:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067392-FisherStrand 2020-01-07T21:15:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067412-ClipReads 2020-01-07T21:13:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067432-SoftClippedReadFilter 2020-01-07T21:17:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067452-CalculateReadGroupChecksum-Picard 2020-01-07T21:13:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067472-SetNmMdAndUqTags-Picard 2020-01-07T21:16:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067492-CompareMetrics-Picard 2020-01-07T21:14:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067512-FuncotateSegments-BETA 2020-01-07T21:15:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067532-CalculateFingerprintMetrics-Picard 2020-01-07T21:13:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067552-CompareBaseQualities 2020-01-07T21:14:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067572-CollectAlignmentSummaryMetrics-Picard 2020-01-07T21:13:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067592-AnnotateVcfWithBamDepth 2020-01-07T21:13:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067612-CollectSequencingArtifactMetrics-Picard 2020-01-07T21:14:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067632-GatherVcfs-Picard 2020-01-07T21:15:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067672-ExtractSequences-Picard 2020-01-07T21:14:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067692-CpxVariantReInterpreterSpark-BETA 2020-01-07T21:14:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067712-MakeSitesOnlyVcf-Picard 2020-01-07T21:15:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067732-IntervalListTools-Picard 2020-01-07T21:15:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067752-LeftAlignIndels 2020-01-07T21:15:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067772-FilterIntervals-BETA 2020-01-07T21:15:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067792-MappingQualityNotZeroReadFilter 2020-01-07T21:15:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067812-NonNFastaSize-Picard 2020-01-07T21:16:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067832-FilterMutectCalls 2020-01-07T21:15:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067852-BaseRecalibratorSpark-BETA 2020-01-07T21:13:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067872-SelectVariants 2020-01-07T21:16:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067892-AccumulateVariantCallingMetrics-Picard 2020-01-07T21:13:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067912-ReadGroupReadFilter 2020-01-07T21:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067932-CollectQualityYieldMetricsSpark-BETA 2020-01-07T21:14:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067952-CreateHadoopBamSplittingIndex-BETA 2020-01-07T21:14:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067972-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-01-07T21:13:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037067992-HaplotypeCaller 2020-01-07T21:15:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068012-ReplaceSamHeader-Picard 2020-01-07T21:16:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068032-CollectIlluminaLaneMetrics-Picard 2020-01-07T21:14:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068052-PolymorphicNuMT 2020-01-07T21:16:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068072-MarkDuplicatesGATK-EXPERIMENTAL 2020-01-07T21:15:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068092-SetNmAndUqTags-Picard 2020-01-07T21:16:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068112-PathSeqBwaSpark 2020-01-07T21:16:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068132-MeanQualityByCycleSpark-BETA 2020-01-07T21:16:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068152-FragmentLength 2020-01-07T21:15:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068172-CollectBaseDistributionByCycle-Picard 2020-01-07T21:14:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068192-ReblockGVCF-EXPERIMENTAL 2020-01-07T21:16:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068212-FixMisencodedBaseQualityReads 2020-01-07T21:15:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068232-LeftAlignAndTrimVariants 2020-01-07T21:15:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068252-BedToIntervalList-Picard 2020-01-07T21:13:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068272-CompareDuplicatesSpark-BETA 2020-01-07T21:14:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068292-OriginalAlignment 2020-01-07T21:16:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068312-CreateSequenceDictionary-Picard 2020-01-07T21:14:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068332-GoodCigarReadFilter 2020-01-07T21:15:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068352-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:16:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068372-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:15:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068392-PostprocessGermlineCNVCalls-BETA 2020-01-07T21:16:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068412-NotSupplementaryAlignmentReadFilter 2020-01-07T21:16:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068432-GenotypeSummaries 2020-01-07T21:15:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068452-FlagStatSpark-BETA 2020-01-07T21:15:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068472-CollectWgsMetrics-Picard 2020-01-07T21:14:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068492-PairedReadFilter 2020-01-07T21:16:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068512-AS-ReadPosRankSumTest 2020-01-07T21:13:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068532-GetPileupSummaries-BETA 2020-01-07T21:15:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068552-FifoBuffer-Picard 2020-01-07T21:14:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068572-ExcessHet 2020-01-07T21:14:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068592-LikelihoodRankSumTest 2020-01-07T21:15:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068612-DownsampleSam-Picard 2020-01-07T21:14:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068632-CompareSAMs-Picard 2020-01-07T21:14:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068652-BQSRPipelineSpark-BETA 2020-01-07T21:13:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068672-PossibleDeNovo 2020-01-07T21:16:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068692-CollectInsertSizeMetricsSpark-BETA 2020-01-07T21:14:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068712-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:17:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068732-IntervalListToBed-Picard 2020-01-07T21:15:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068752-ApplyVQSR 2020-01-07T21:13:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068772-UpdateVcfSequenceDictionary-Picard 2020-01-07T21:17:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068792-ScatterIntervalsByNs-Picard 2020-01-07T21:16:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068812-AS-InbreedingCoeff 2020-01-07T21:13:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068832-VcfFormatConverter-Picard 2020-01-07T21:17:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068852-CollectVariantCallingMetrics-Picard 2020-01-07T21:14:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068872-CollectGcBiasMetrics-Picard 2020-01-07T21:14:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068912-ReadPosition 2020-01-07T21:16:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068932-MateOnSameContigOrNoMappedMateReadFilter 2020-01-07T21:15:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068952-Coverage 2020-01-07T21:14:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068972-ReadStrandFilter 2020-01-07T21:16:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037068992-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-01-07T21:14:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069012-CalculateGenotypePosteriors 2020-01-07T21:13:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069032-ValidateVariants 2020-01-07T21:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069052-ExtractSVEvidenceSpark-BETA 2020-01-07T21:14:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069072-CNNScoreVariants-EXPERIMENTAL 2020-01-07T21:13:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069092-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-01-07T21:16:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069112-MethylationTypeCaller-EXPERIMENTAL 2020-01-07T21:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069132-CombineSegmentBreakpoints-EXPERIMENTAL 2020-01-07T21:14:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069152-FlagStat 2020-01-07T21:15:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069172-BaitDesigner-Picard 2020-01-07T21:13:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069192-InbreedingCoeff 2020-01-07T21:15:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069212-ReadLengthEqualsCigarLengthReadFilter 2020-01-07T21:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069232-PrintVariantsSpark-BETA 2020-01-07T21:16:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069252-ValidateSamFile-Picard 2020-01-07T21:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069272-FastqToSam-Picard 2020-01-07T21:14:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069292-ReadGroupBlackListReadFilter 2020-01-07T21:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069312-StrandArtifact 2020-01-07T21:17:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069332-CollectRnaSeqMetrics-Picard 2020-01-07T21:14:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069352-GatherVcfsCloud-BETA 2020-01-07T21:15:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069372-AnnotateIntervals-BETA 2020-01-07T21:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069392-RevertSam-Picard 2020-01-07T21:16:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069412-AS-MappingQualityRankSumTest 2020-01-07T21:13:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069432-BaseRecalibratorSparkSharded-EXPERIMENTAL 2020-01-07T21:13:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069452-SeqIsStoredReadFilter 2020-01-07T21:16:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069472-NonZeroReferenceLengthAlignmentReadFilter 2020-01-07T21:16:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069492-CollectBaseDistributionByCycleSpark-BETA 2020-01-07T21:14:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069512-VariantRecalibrator 2020-01-07T21:17:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069532-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-01-07T21:14:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069552-PlotDenoisedCopyRatios-BETA 2020-01-07T21:16:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069572-UnmarkDuplicates 2020-01-07T21:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069592-SplitNCigarReads 2020-01-07T21:17:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069612-FilterFuncotations-EXPERIMENTAL 2020-01-07T21:15:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069632-CNNVariantTrain-EXPERIMENTAL 2020-01-07T21:13:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069652-TandemRepeat 2020-01-07T21:17:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069672-AddCommentsToBam-Picard 2020-01-07T21:13:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069692-AnalyzeSaturationMutagenesis-BETA 2020-01-07T21:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069712-AS-QualByDepth 2020-01-07T21:13:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069732-Concordance-BETA 2020-01-07T21:14:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069752-FragmentLengthReadFilter 2020-01-07T21:15:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069772-BuildBamIndex-Picard 2020-01-07T21:13:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069792-CollectRrbsMetrics-Picard 2020-01-07T21:14:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069812-ReferenceBases 2020-01-07T21:16:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069832-IndexFeatureFile 2024-07-25T15:46:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069852-MetricsReadFilter 2020-01-07T21:16:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069872-QualityScoreDistributionSpark-BETA 2020-01-07T21:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069892-DepthPerSampleHC 2020-01-07T21:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069912-ConvertSequencingArtifactToOxoG-Picard 2020-01-07T21:14:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069932-RenameSampleInVcf-Picard 2020-01-07T21:16:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069952-MappingQualityAvailableReadFilter 2020-01-07T21:15:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069972-CollectOxoGMetrics-Picard 2020-01-07T21:14:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037069992-CreateReadCountPanelOfNormals-BETA 2020-01-07T21:14:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037070012-CountBasesSpark-BETA 2020-01-07T21:14:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037070032-PrintReadsSpark-BETA 2020-01-07T21:16:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037070052-ASEReadCounter 2020-01-07T21:13:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224392-MeanQualityByCycle-Picard 2019-12-05T15:10:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224412-CollectHiSeqXPfFailMetrics-Picard 2019-12-05T15:10:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224432-Funcotator 2023-11-02T16:34:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224452-CollectQualityYieldMetrics-Picard 2019-12-05T15:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224472-PathSeqPipelineSpark 2024-09-05T09:24:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224492-CalcMetadataSpark-BETA 2019-12-05T15:10:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224512-AlignmentAgreesWithHeaderReadFilter 2019-12-05T15:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224532-AS-StrandOddsRatio 2019-12-05T15:10:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224552-FilterVcf-Picard 2019-12-05T15:05:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224572-VariantEval-BETA 2019-12-05T15:10:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224592-VariantEval-BETA 2019-12-05T15:05:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224632-LiftOverIntervalList-Picard 2019-12-05T15:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224652-VariantAnnotator-BETA 2019-12-05T15:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224672-FilterSamReads-Picard 2019-12-05T15:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224692-CollectMultipleMetricsSpark-BETA 2019-12-05T15:10:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224712--Tool-Documentation-Index 2022-08-23T18:17:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224732-CheckFingerprint-Picard 2019-12-05T15:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224752-HasReadGroupReadFilter 2019-12-05T15:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224772-DetermineGermlineContigPloidy 2019-12-05T15:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224792-FindBreakpointEvidenceSpark-BETA 2019-12-05T15:10:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224812-MappingQuality 2019-12-05T15:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224832-UpdateVCFSequenceDictionary 2019-12-05T15:10:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224852-ClusterCrosscheckMetrics-Picard 2019-12-05T15:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224872-ClipReads 2019-12-05T15:10:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224892-CollectSamErrorMetrics-Picard 2019-12-05T15:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224912-GetSampleName 2019-12-05T15:10:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224932-MarkDuplicatesSpark 2021-09-14T08:04:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224952-CalculateReadGroupChecksum-Picard 2019-12-05T15:10:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224972-CalculateReadGroupChecksum-Picard 2019-12-05T15:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037224992-FuncotateSegments-BETA 2019-12-05T15:11:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225012-GatherBamFiles-Picard 2019-12-05T15:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225032-CalculateFingerprintMetrics-Picard 2019-12-05T15:06:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225052-PathSeqBuildReferenceTaxonomy 2019-12-05T15:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225072-AS-FisherStrand 2019-12-05T15:11:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225092-BwaSpark-BETA 2019-12-05T15:11:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225112-CollectAlignmentSummaryMetrics-Picard 2019-12-05T15:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225132-GatherVcfs-Picard 2019-12-05T15:06:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225152-MarkDuplicatesWithMateCigar-Picard 2019-12-05T15:11:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225172-AlleleFrequency 2022-12-01T07:36:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225192-CalculateContamination 2019-12-05T15:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225212-ApplyBQSR 2019-12-05T15:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225232-PathSeqBuildKmers 2019-12-05T15:11:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225252-CollectInsertSizeMetrics-Picard 2019-12-05T15:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225272-StrandBiasBySample 2019-12-05T15:11:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225292-SortSamSpark-BETA 2019-12-05T15:11:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225312-FilterIntervals 2019-12-05T15:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225352-MappingQualityNotZeroReadFilter 2019-12-05T15:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225372-SplitSamByNumberOfReads-Picard 2019-12-05T15:11:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225392-MateDifferentStrandReadFilter 2019-12-05T15:11:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225412-FilterMutectCalls 2019-12-05T15:11:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225432-SelectVariants 2019-12-05T15:11:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225452-AccumulateVariantCallingMetrics-Picard 2019-12-05T15:07:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225472-IlluminaBasecallsToSam-Picard 2019-12-05T15:11:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225492-ReadGroupReadFilter 2019-12-05T15:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225512-MappingQualityReadFilter 2019-12-05T15:11:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225532-CollectQualityYieldMetricsSpark-BETA 2019-12-05T15:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225552-PlatformUnitReadFilter 2019-12-05T15:07:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225572-PlatformUnitReadFilter 2019-12-05T15:07:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225592-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-12-05T15:11:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225612-BwaAndMarkDuplicatesPipelineSpark-BETA 2019-12-05T15:07:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller 2025-07-01T14:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225652-ReadsPipelineSpark-BETA 2019-12-05T15:11:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225672-CountFalsePositives-BETA 2019-12-05T15:11:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225692-CountBasesInReference 2019-12-05T15:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225712-VcfToIntervalList-Picard 2019-12-05T15:11:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225732-VcfToIntervalList-Picard 2019-12-05T15:07:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225752-SetNmAndUqTags-Picard 2019-12-05T15:11:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225772-MarkIlluminaAdapters-Picard 2019-12-05T15:11:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225792-MatchingBasesAndQualsReadFilter 2019-12-05T15:07:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225812-CollectTargetedPcrMetrics-Picard 2019-12-05T15:11:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225832-MergeBamAlignment-Picard 2019-12-05T15:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225852-FixMisencodedBaseQualityReads 2019-12-05T15:11:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225872-LeftAlignAndTrimVariants 2021-03-23T15:33:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225892-ModelSegments 2019-12-05T15:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225912-RemoveNearbyIndels 2019-12-05T15:11:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225932-FilterByOrientationBias-EXPERIMENTAL 2019-12-05T15:11:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225952-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2019-12-05T15:11:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225972-MarkDuplicates-Picard 2019-12-05T15:11:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037225992-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-12-05T15:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226012-PositionBasedDownsampleSam-Picard 2019-12-05T15:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226032-ReorderSam-Picard 2019-12-05T15:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226052-NotSupplementaryAlignmentReadFilter 2019-12-05T15:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226072-GenotypeSummaries 2019-12-05T15:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226092-FlagStatSpark 2019-12-05T15:11:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226112-FilterAlignmentArtifacts-EXPERIMENTAL 2019-12-05T15:11:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226132-CollectWgsMetrics-Picard 2019-12-05T15:11:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226152-AS-ReadPosRankSumTest 2019-12-05T15:12:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226172-ExcessHet 2019-12-05T15:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226192-VariantFiltration 2019-12-05T15:12:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226212-LikelihoodRankSumTest 2019-12-05T15:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226232-DownsampleSam-Picard 2019-12-05T15:12:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226252-ClippingRankSumTest 2019-12-05T15:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226272-CollectInsertSizeMetricsSpark-BETA 2019-12-05T15:12:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226292-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2019-12-05T15:12:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226312-IntervalListToBed-Picard 2019-12-05T15:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226332-ApplyVQSR 2019-12-05T15:12:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226352-GermlineCNVCaller 2019-12-05T15:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226372-UpdateVcfSequenceDictionary-Picard 2019-12-05T15:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226392-ReadNameReadFilter 2019-12-05T15:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226412-ScatterIntervalsByNs-Picard 2019-12-05T15:12:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226432-PlatformReadFilter 2019-12-05T15:08:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226452-VcfFormatConverter-Picard 2019-12-05T15:12:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard 2024-05-10T07:04:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226492-CollectVariantCallingMetrics-Picard 2019-12-05T15:08:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226512-LiftoverVcf-Picard 2019-12-05T15:12:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226532-AddOATag-Picard 2019-12-05T15:12:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226552-MateOnSameContigOrNoMappedMateReadFilter 2019-12-05T15:12:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226572-ReadStrandFilter 2019-12-05T15:08:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226592-CalculateGenotypePosteriors 2023-12-14T07:58:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226612-MergeVcfs-Picard 2019-12-05T15:12:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226632-ValidateVariants 2019-12-05T15:12:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226672-CNNScoreVariants 2025-01-14T17:18:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226692-MethylationTypeCaller-EXPERIMENTAL 2019-12-05T15:12:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226712-PreprocessIntervals 2019-12-05T15:12:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226732-QualityScoreDistribution-Picard 2019-12-05T15:08:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226772-SortVcf-Picard 2019-12-05T15:12:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226792-FastqToSam-Picard 2020-03-04T13:09:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226812-ReadGroupBlackListReadFilter 2019-12-05T15:09:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226832-CollectIlluminaBasecallingMetrics-Picard 2019-12-05T15:09:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226852-FuncotatorDataSourceDownloader 2019-12-05T15:09:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226872-ConvertHeaderlessHadoopBamShardToBam-BETA 2019-12-05T15:09:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226892-CollectRnaSeqMetrics-Picard 2019-12-05T15:09:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226912-GatherVcfsCloud-BETA 2019-12-05T15:12:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226932-AnnotateIntervals 2019-12-05T15:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226952-RevertSam-Picard 2019-12-05T15:12:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226972-PassesVendorQualityCheckReadFilter 2019-12-05T15:09:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037226992-SplitReads 2019-12-05T15:12:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227012-AS-MappingQualityRankSumTest 2019-12-05T15:12:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227032-AS-MappingQualityRankSumTest 2019-12-05T15:09:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227052-FixCallSetSampleOrdering-EXPERIMENTAL 2019-12-05T15:12:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227072-BaseQuality 2019-12-05T15:09:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227092-PlotDenoisedCopyRatios 2019-12-05T15:09:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227112-SplitIntervals 2019-12-05T15:12:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227132-UnmarkDuplicates 2019-12-05T15:12:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227152-StructuralVariationDiscoveryPipelineSpark-BETA 2019-12-05T15:12:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227172-ProperlyPairedReadFilter 2019-12-05T15:09:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227192-CigarContainsNoNOperator 2019-12-05T15:09:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227212-FilterFuncotations-EXPERIMENTAL 2019-12-05T15:13:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227232-SplitSamByLibrary-Picard 2019-12-05T15:13:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227272-CNNVariantTrain-EXPERIMENTAL 2019-12-05T15:13:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227292-TandemRepeat 2019-12-05T15:09:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227312-AddCommentsToBam-Picard 2019-12-05T15:13:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227332-AS-QualByDepth 2019-12-05T15:13:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227352-Concordance-BETA 2019-12-05T15:13:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227372-FragmentLengthReadFilter 2019-12-05T15:09:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227392-BuildBamIndex-Picard 2019-12-05T15:13:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227412-NotSecondaryAlignmentReadFilter 2019-12-05T15:09:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227432-ReferenceBases 2019-12-05T15:09:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227452-ValidAlignmentEndReadFilter 2019-12-05T15:13:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227472-FastaReferenceMaker 2019-12-05T15:13:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227492-QualityScoreDistributionSpark-BETA 2019-12-05T15:13:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227512-DepthPerSampleHC 2021-07-13T00:22:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227532-OrientationBiasReadCounts 2019-12-05T15:09:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227552-CollectOxoGMetrics-Picard 2019-12-05T15:10:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227572-CreateReadCountPanelOfNormals 2019-12-05T15:10:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227592-PrintReadsSpark 2019-12-05T15:13:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227612-ASEReadCounter 2019-12-05T15:13:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227632-FilterVariantTranches 2019-12-05T15:13:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227652-CreateSomaticPanelOfNormals-BETA 2019-12-05T15:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227672-CheckPileup 2019-12-05T15:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037227692-ReadLengthReadFilter 2019-12-05T15:10:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259451-CollectIndependentReplicateMetrics-Picard-BETA 2020-01-07T20:52:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259471-ChromosomeCounts 2020-01-07T20:52:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259491-LibraryReadFilter 2020-01-07T20:54:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259511-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2020-01-07T20:52:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259531-NonChimericOriginalAlignmentReadFilter 2020-01-07T20:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259551-OverclippedReadFilter 2020-01-07T20:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259571-SampleReadFilter 2020-01-07T20:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259591-RMSMappingQuality 2020-01-07T20:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259611-FirstOfPairReadFilter 2020-01-07T20:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259631-CollectQualityYieldMetrics-Picard 2020-01-07T20:52:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259651-CalcMetadataSpark-BETA 2020-01-07T20:52:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259671-AnnotatePairOrientation-BETA 2020-01-07T20:52:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259691-VariantEval-BETA 2020-01-07T20:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259711-FixVcfHeader-Picard 2020-01-07T20:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259731-CollectHsMetrics-Picard 2020-01-07T20:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259751-GnarlyGenotyper-BETA 2020-01-07T20:54:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259771-AnnotateVcfWithExpectedAlleleFraction 2020-01-07T20:52:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259791-CountVariants 2020-01-07T20:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259811-NotDuplicateReadFilter 2020-01-07T20:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259831-VariantAnnotator-BETA 2020-01-07T20:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259851-FilterSamReads-Picard 2020-01-07T20:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259871-CollectMultipleMetricsSpark-BETA 2020-01-07T20:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259891-CountBases 2020-01-07T20:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259911-StrandOddsRatio 2020-01-07T20:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259931--Tool-Documentation-Index 2020-01-07T20:51:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259951-UniqueAltReadCount 2020-01-07T20:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259971-QualByDepth 2020-01-07T20:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037259991-NormalizeFasta-Picard 2020-01-07T20:54:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260011-AS-RMSMappingQuality 2020-01-07T20:52:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260031-CNNVariantWriteTensors-EXPERIMENTAL 2020-01-07T20:52:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260051-CountVariantsSpark-BETA 2020-01-07T20:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260071-SamFormatConverter-Picard 2020-01-07T20:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260091-MarkDuplicatesSpark-BETA 2020-01-07T20:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260111-SetNmMdAndUqTags-Picard 2020-01-07T20:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260131-GatherBamFiles-Picard 2020-01-07T20:53:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260151-PathSeqBuildReferenceTaxonomy 2020-01-07T20:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260171-AnnotateVcfWithBamDepth 2020-01-07T20:52:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260191-CollectSequencingArtifactMetrics-Picard 2020-01-07T20:52:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260231-ExtractSequences-Picard 2020-01-07T20:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260251-ApplyBQSR 2020-01-07T20:52:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260271-CollectInsertSizeMetrics-Picard 2020-01-07T20:52:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260291-CollectReadCounts-BETA 2020-01-07T20:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260311-SortSamSpark-BETA 2020-01-07T20:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260331-LeftAlignIndels 2020-01-07T20:54:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260351-FilterIntervals-BETA 2020-01-07T20:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260371-MappingQualityNotZeroReadFilter 2020-01-07T20:54:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260391-HaplotypeCallerSpark-BETA 2020-01-07T20:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260411-CollectJumpingLibraryMetrics-Picard 2020-01-07T20:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260431-SplitSamByNumberOfReads-Picard 2020-01-07T20:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260451-MateDifferentStrandReadFilter 2020-01-07T20:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260471-NonNFastaSize-Picard 2020-01-07T20:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260491-BaseRecalibratorSpark-BETA 2020-01-07T20:52:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260511-SelectVariants 2020-01-07T20:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260531-AccumulateVariantCallingMetrics-Picard 2020-01-07T20:51:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260551-ReadGroupReadFilter 2020-01-07T20:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260571-PlatformUnitReadFilter 2020-01-07T20:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260591-CreateHadoopBamSplittingIndex-BETA 2020-01-07T20:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260611-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-01-07T20:52:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260631-ValidAlignmentStartReadFilter 2020-01-07T20:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260651-ReadsPipelineSpark-BETA 2020-01-07T20:55:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260671-ReplaceSamHeader-Picard 2020-01-07T20:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260691-CountFalsePositives-BETA 2020-01-07T20:53:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260711-CollectIlluminaLaneMetrics-Picard 2020-01-07T20:52:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260731-CountBasesInReference 2020-01-07T20:53:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260751-PolymorphicNuMT 2020-01-07T20:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260771-MarkDuplicatesGATK-EXPERIMENTAL 2020-01-07T20:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260791-PathSeqBwaSpark 2020-01-07T20:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260811-SampleList 2020-01-07T20:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260831-MatchingBasesAndQualsReadFilter 2020-01-07T20:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260851-MeanQualityByCycleSpark-BETA 2020-01-07T20:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260871-FragmentLength 2020-01-07T20:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260891-CheckIlluminaDirectory-Picard 2020-01-07T20:52:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260911-CollectTargetedPcrMetrics-Picard 2020-01-07T20:52:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260931-CollectBaseDistributionByCycle-Picard 2020-01-07T20:52:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260951-FixMisencodedBaseQualityReads 2020-01-07T20:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260971-ModelSegments-BETA 2020-01-07T20:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037260991-RevertSamSpark-BETA 2020-01-07T20:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261011-AmbiguousBaseReadFilter 2020-01-07T20:51:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261031-CollectRawWgsMetrics-Picard 2020-01-07T20:52:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261051-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-01-07T20:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261071-OriginalAlignment 2020-01-07T20:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261091-VcfToAdpc-Picard 2020-01-07T20:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261111-GoodCigarReadFilter 2020-01-07T20:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261131-PositionBasedDownsampleSam-Picard 2020-01-07T20:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261151-ReorderSam-Picard 2020-01-07T20:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261171-NotSupplementaryAlignmentReadFilter 2020-01-07T20:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261191-GenotypeSummaries 2020-01-07T20:54:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261211-FlagStatSpark-BETA 2020-01-07T20:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261231-FilterAlignmentArtifacts-EXPERIMENTAL 2020-01-07T20:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261251-CollectWgsMetrics-Picard 2020-01-07T20:52:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261271-PairedReadFilter 2020-01-07T20:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261291-GetPileupSummaries-BETA 2020-01-07T20:54:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261311-ExcessHet 2020-07-17T19:29:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261331-LikelihoodRankSumTest 2020-01-07T20:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261371-BaseRecalibrator 2020-01-07T20:52:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261391-RevertBaseQualityScores 2020-01-07T20:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261411-GatherTranches-BETA 2020-01-07T20:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261431-DownsampleSam-Picard 2020-01-07T20:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261451-ClippingRankSumTest 2020-01-07T20:52:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261471-CompareSAMs-Picard 2020-01-07T20:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261491-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T20:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261531-DenoiseReadCounts-BETA 2020-01-07T20:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261551-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T20:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261571-IntervalListToBed-Picard 2020-01-07T20:54:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261591-MappingQualityZero 2020-01-07T20:54:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261611-CallCopyRatioSegments-BETA 2020-01-07T20:52:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261631-PlatformReadFilter 2020-01-07T20:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261651-BamIndexStats-Picard 2020-01-07T20:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261671-FilterMutectCalls-BETA 2020-01-07T20:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261691-Mutect2-BETA 2020-01-07T20:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261711-PlotModeledSegments-BETA 2020-01-07T20:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261731-CollectVariantCallingMetrics-Picard 2020-01-07T20:52:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261751-LiftoverVcf-Picard 2020-01-07T20:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261771-MateOnSameContigOrNoMappedMateReadFilter 2020-01-07T20:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261791-Coverage 2020-01-07T20:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261811-ReadStrandFilter 2020-01-07T20:55:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261831-MergeVcfs-Picard 2020-01-07T20:54:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261851-CollectMultipleMetrics-Picard 2020-01-07T20:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261871-CollectAllelicCounts-BETA 2020-01-07T20:52:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261891-CNNScoreVariants-EXPERIMENTAL 2020-01-07T20:52:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261931-PreprocessIntervals-BETA 2020-01-07T20:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261951-QualityScoreDistribution-Picard 2020-01-07T20:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261971-CombineSegmentBreakpoints-EXPERIMENTAL 2020-01-07T20:52:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037261991-FlagStat 2020-01-07T20:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262011-InbreedingCoeff 2020-01-07T20:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262031-FixMateInformation-Picard 2020-01-07T20:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262051-PrintVariantsSpark-BETA 2020-01-07T20:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262071-ValidateSamFile-Picard 2020-01-07T20:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262091-ReadGroupBlackListReadFilter 2020-01-07T20:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262111-FuncotatorDataSourceDownloader-BETA 2020-01-07T20:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262131-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-01-07T20:53:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262151-MergeSamFiles-Picard 2020-01-07T20:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262171-AnnotateIntervals-BETA 2020-01-07T20:51:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262191-CollectFragmentCounts-BETA 2020-01-07T20:52:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262211-BaseRecalibratorSparkSharded-EXPERIMENTAL 2020-01-07T20:52:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262231-BaseQuality 2020-01-07T20:52:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262251-SeqIsStoredReadFilter 2020-01-07T20:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262271-NonZeroReferenceLengthAlignmentReadFilter 2020-01-07T20:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262291-VariantRecalibrator 2020-01-07T20:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262311-PlotDenoisedCopyRatios-BETA 2020-01-07T20:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262331-SplitIntervals 2020-01-07T20:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262371-EvaluateInfoFieldConcordance-BETA 2020-01-07T20:53:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262391-SplitNCigarReads 2020-01-07T20:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262411-PileupSpark-BETA 2020-01-07T20:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262431-ProperlyPairedReadFilter 2020-01-07T20:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262451-FilterFuncotations-EXPERIMENTAL 2020-01-07T20:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262471-GenotypeGVCFs 2020-01-07T20:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262491-AddCommentsToBam-Picard 2020-01-07T20:51:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262511-AnalyzeSaturationMutagenesis-BETA 2020-01-07T20:51:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262531-AS-QualByDepth 2020-01-07T20:52:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262551-AS-BaseQualityRankSumTest 2020-01-07T20:52:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262571-FragmentLengthReadFilter 2020-01-07T20:53:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262591-BuildBamIndex-Picard 2020-01-07T20:52:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262611-NotSecondaryAlignmentReadFilter 2020-01-07T20:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262631-ReferenceBases 2020-01-07T20:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile 2020-01-07T20:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262671-QualityScoreDistributionSpark-BETA 2020-01-07T20:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262691-CountNs 2020-01-07T20:53:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262711-MappingQualityAvailableReadFilter 2020-01-07T20:54:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262731-CollectOxoGMetrics-Picard 2020-01-07T20:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262751-CreateReadCountPanelOfNormals-BETA 2020-01-07T20:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262771-CountBasesSpark-BETA 2020-01-07T20:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262791-ASEReadCounter 2020-01-07T20:52:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262811-CheckPileup 2020-01-07T20:52:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037262831-ReadLengthReadFilter 2020-01-07T20:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267331-CollectIndependentReplicateMetrics-Picard-BETA 2020-01-07T20:44:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267351-LibraryReadFilter 2020-01-07T20:49:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267371-NonChimericOriginalAlignmentReadFilter 2020-01-07T20:50:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267391-GenotypeConcordance-Picard 2020-01-07T20:49:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267411-OverclippedReadFilter 2020-01-07T20:50:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267431-BwaMemIndexImageCreator 2020-01-07T20:43:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267451-WellformedReadFilter 2020-01-07T20:51:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267491-PathSeqPipelineSpark 2020-01-07T20:50:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267511-CalcMetadataSpark-BETA 2020-01-07T20:43:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267531-AlignmentAgreesWithHeaderReadFilter 2020-01-07T20:43:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267551-AS-StrandOddsRatio 2020-01-07T20:43:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267571-FilterVcf-Picard 2020-01-07T20:49:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267591-AnnotatePairOrientation-BETA 2020-01-07T20:43:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267651-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T20:51:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267671-CountReads 2020-01-07T20:48:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267711-CollectHsMetrics-Picard 2020-01-07T20:44:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267731-GnarlyGenotyper-BETA 2020-01-07T20:49:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267771-AnnotateVcfWithExpectedAlleleFraction 2020-01-07T20:43:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267791-AllowAllReadsReadFilter 2020-01-07T20:43:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267811-LiftOverIntervalList-Picard 2020-01-07T20:49:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267851-BamToBfq-Picard 2020-01-07T20:43:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267871-VariantAnnotator-BETA 2020-01-07T20:51:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267931-CollectMultipleMetricsSpark-BETA 2020-01-07T20:44:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267951-CountBases 2020-01-07T20:44:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267971-StrandOddsRatio 2020-01-07T20:51:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037267991-FindBreakpointEvidenceSpark-BETA 2020-01-07T20:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268011-MappingQuality 2020-01-07T20:50:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268031-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T20:49:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268051-NormalizeFasta-Picard 2020-01-07T20:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268071-CNNVariantWriteTensors-EXPERIMENTAL 2020-01-07T20:43:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268091-CountVariantsSpark-BETA 2020-01-07T20:48:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268111-UpdateVCFSequenceDictionary 2020-01-07T20:51:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268131-SamFormatConverter-Picard 2020-01-07T20:51:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268151-ClusterCrosscheckMetrics-Picard 2020-01-07T20:43:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268171-ClipReads 2020-01-07T20:43:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268191-CollectSamErrorMetrics-Picard 2020-01-07T20:44:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268231-CalculateReadGroupChecksum-Picard 2020-01-07T20:43:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268251-SortReadFileSpark-BETA 2020-01-07T20:51:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268271-SetNmMdAndUqTags-Picard 2020-01-07T20:51:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268291-CompareMetrics-Picard 2020-01-07T20:44:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268311-FuncotateSegments-BETA 2020-01-07T20:49:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268351-AS-FisherStrand 2020-01-07T20:43:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268371-BwaSpark-BETA 2020-01-07T20:43:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268391-CollectAlignmentSummaryMetrics-Picard 2020-01-07T20:44:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268411-AnnotateVcfWithBamDepth 2020-01-07T20:43:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268431-GatherVcfs-Picard 2020-01-07T20:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268451-ExtractSequences-Picard 2020-01-07T20:49:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268471-GatherBQSRReports 2020-01-07T20:49:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268491-CalculateContamination 2020-01-07T20:43:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268511-ApplyBQSR 2020-01-07T20:43:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268531-PathSeqBuildKmers 2020-01-07T20:50:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268551-MakeSitesOnlyVcf-Picard 2020-01-07T20:50:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268571-StrandBiasBySample 2020-01-07T20:51:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268591-CollectReadCounts-BETA 2020-01-07T20:44:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268611-FilterIntervals-BETA 2020-01-07T20:49:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268631-MappingQualityRankSumTest 2020-01-07T20:50:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268651-HaplotypeCallerSpark-BETA 2020-01-07T20:49:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268671-CollectJumpingLibraryMetrics-Picard 2020-01-07T20:44:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268691-SplitSamByNumberOfReads-Picard 2020-01-07T20:51:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268711-AccumulateVariantCallingMetrics-Picard 2020-01-07T20:43:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268731-IlluminaBasecallsToSam-Picard 2020-01-07T20:49:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268751-MappingQualityReadFilter 2020-01-07T20:50:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268771-OxoGReadCounts 2020-01-07T20:50:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268791-CreateHadoopBamSplittingIndex-BETA 2020-01-07T20:48:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268811-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-01-07T20:43:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268831-CrosscheckReadGroupFingerprints-Picard 2020-01-07T20:48:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268851-ValidAlignmentStartReadFilter 2020-01-07T20:51:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268871-CountBasesInReference 2020-01-07T20:48:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268891-PathSeqBwaSpark 2025-03-22T01:35:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268911-SampleList 2020-01-07T20:51:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268931-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-01-07T20:49:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268951-FragmentLength 2020-01-07T20:49:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268971-CheckIlluminaDirectory-Picard 2020-01-07T20:43:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037268991-FixMisencodedBaseQualityReads 2020-01-07T20:49:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269031-AmbiguousBaseReadFilter 2020-01-07T20:43:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269051-CompareDuplicatesSpark-BETA 2020-01-07T20:44:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269071-CollectRawWgsMetrics-Picard 2020-01-07T20:44:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269091-FilterByOrientationBias-EXPERIMENTAL 2020-01-07T20:49:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269111-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-01-07T20:51:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269131-OriginalAlignment 2020-01-07T20:50:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269151-VcfToAdpc-Picard 2020-01-07T20:51:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269171-GoodCigarReadFilter 2020-01-07T20:49:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269191-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T20:51:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269211-PositionBasedDownsampleSam-Picard 2020-01-07T20:50:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269231-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T20:49:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269251-ReorderSam-Picard 2020-01-07T20:51:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269271-PostprocessGermlineCNVCalls-BETA 2020-01-07T20:50:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269291-NotSupplementaryAlignmentReadFilter 2020-01-07T20:50:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269311-FlagStatSpark-BETA 2020-01-07T20:49:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269331-FilterAlignmentArtifacts-EXPERIMENTAL 2020-01-07T20:49:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269351-CollectWgsMetrics-Picard 2022-01-04T14:24:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269371-AS-ReadPosRankSumTest 2020-01-07T20:43:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269391-VariantFiltration 2020-01-07T20:51:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269411-GatherTranches-BETA 2020-01-07T20:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269451-DownsampleSam-Picard 2020-01-07T20:49:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269471-ClippingRankSumTest 2020-01-07T20:43:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269511-CompareSAMs-Picard 2020-01-07T20:44:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269551-BQSRPipelineSpark-BETA 2020-01-07T20:43:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269611-PossibleDeNovo 2020-01-07T20:50:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269651-DenoiseReadCounts-BETA 2020-01-07T20:49:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269691-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T20:51:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269711-IntervalListToBed-Picard 2020-01-07T20:49:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269731-UpdateVcfSequenceDictionary-Picard 2020-01-07T20:51:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269751-PlatformReadFilter 2020-01-07T20:50:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269771-FilterMutectCalls-BETA 2020-01-07T20:49:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269791-Mutect2-BETA 2020-01-07T20:50:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269811-AddOrReplaceReadGroups-Picard 2020-01-07T20:43:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269831-PlotModeledSegments-BETA 2020-01-07T20:50:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269851-CollectVariantCallingMetrics-Picard 2020-01-07T20:44:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269871-LiftoverVcf-Picard 2020-01-07T20:49:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269891-MateOnSameContigOrNoMappedMateReadFilter 2020-01-07T20:50:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269911-Coverage 2020-01-07T20:48:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269931-ApplyBQSRSpark-BETA 2020-01-07T20:43:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269951-ExtractSVEvidenceSpark-BETA 2020-01-07T20:49:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269971-CNNScoreVariants-EXPERIMENTAL 2020-01-07T20:43:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037269991-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-01-07T20:51:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270031-MethylationTypeCaller-EXPERIMENTAL 2020-01-07T20:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270051-PreprocessIntervals-BETA 2020-01-07T20:50:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270071-QualityScoreDistribution-Picard 2020-01-07T20:50:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270111-FlagStat 2020-01-07T20:49:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270151-InbreedingCoeff 2020-01-07T20:49:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270171-ReadLengthEqualsCigarLengthReadFilter 2020-01-07T20:50:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270191-PrintVariantsSpark-BETA 2020-01-07T20:50:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270211-ValidateSamFile-Picard 2020-01-07T20:51:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270251-ReadGroupBlackListReadFilter 2020-01-07T20:50:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270331-SortSam-Picard 2020-01-07T20:51:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270371-MergeSamFiles-Picard 2020-01-07T20:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270391-CollectRnaSeqMetrics-Picard 2020-01-07T20:44:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270411-AnnotateIntervals-BETA 2020-01-07T20:43:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270431-PathSeqScoreSpark 2020-01-07T20:50:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270451-RevertSam-Picard 2020-01-07T20:51:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270471-PassesVendorQualityCheckReadFilter 2020-01-07T20:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270511-SplitReads 2020-01-07T20:51:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270551-FixCallSetSampleOrdering-EXPERIMENTAL 2020-01-07T20:49:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270571-BaseRecalibratorSparkSharded-EXPERIMENTAL 2020-01-07T20:43:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270591-ReadPosRankSumTest 2020-01-07T20:50:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270631-IntervalOverlapReadFilter 2020-01-07T20:49:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270651-NonZeroReferenceLengthAlignmentReadFilter 2020-01-07T20:50:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270671-PathSeqFilterSpark 2020-01-07T20:50:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270711-UnmarkDuplicates 2020-01-07T20:51:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270731-EvaluateInfoFieldConcordance-BETA 2020-01-07T20:49:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270751-NonZeroFragmentLengthReadFilter 2020-01-07T20:50:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270771-PileupSpark-BETA 2020-01-07T20:50:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270791-SplitVcfs-Picard 2020-01-07T20:51:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270811-FilterFuncotations-EXPERIMENTAL 2020-01-07T20:49:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270851-SplitSamByLibrary-Picard 2020-01-07T20:51:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270871-CrosscheckFingerprints-Picard 2020-01-07T20:48:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270911-AnalyzeSaturationMutagenesis-BETA 2020-01-07T20:43:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270931-AS-BaseQualityRankSumTest 2020-01-07T20:43:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270951-FragmentLengthReadFilter 2020-01-07T20:49:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270971-CollectRrbsMetrics-Picard 2020-01-07T20:44:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037270991-FindMendelianViolations-Picard 2020-01-07T20:49:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271011-ReferenceBases 2020-01-07T20:51:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271031-MetricsReadFilter 2020-01-07T20:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271051-FastaReferenceMaker 2020-01-07T20:49:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271071-QualityScoreDistributionSpark-BETA 2020-01-07T20:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271091-DepthPerSampleHC 2020-01-07T20:49:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271111-AlleleFraction 2020-01-07T20:43:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271131-RenameSampleInVcf-Picard 2020-01-07T20:51:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271171-MappingQualityAvailableReadFilter 2020-01-07T20:50:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271191-CreateReadCountPanelOfNormals-BETA 2020-01-07T20:48:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271211-CountReadsSpark-BETA 2020-01-07T20:48:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271231-PrintReadsSpark-BETA 2020-01-07T20:50:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271251-ASEReadCounter 2020-01-07T20:43:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271271-FilterVariantTranches-EXPERIMENTAL 2020-01-07T20:49:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271291-GtcToVcf-Picard 2020-01-07T20:49:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271311-ReadLengthReadFilter 2020-01-07T20:50:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037271331-CleanSam-Picard 2020-01-07T20:43:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037420951-CollectIndependentReplicateMetrics-Picard-BETA 2020-01-07T20:56:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037420971-ChromosomeCounts 2020-01-07T20:56:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037420991-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2020-01-07T20:57:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421011-MeanQualityByCycle-Picard 2020-01-07T20:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421031-CollectHiSeqXPfFailMetrics-Picard 2020-01-07T20:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421051-Pileup 2020-01-07T20:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421071-BwaMemIndexImageCreator 2020-01-07T20:56:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421111-WellformedReadFilter 2020-01-07T21:00:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421131-SampleReadFilter 2020-01-07T20:59:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421151-AnalyzeCovariates 2020-01-07T20:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421171-RMSMappingQuality 2020-01-07T20:59:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421191-FirstOfPairReadFilter 2020-01-07T20:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421211-CollectQualityYieldMetrics-Picard 2020-01-07T20:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421231-SecondOfPairReadFilter 2020-01-07T20:59:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421251-AlignmentAgreesWithHeaderReadFilter 2020-01-07T20:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421271-FilterVcf-Picard 2020-01-07T20:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421291-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-01-07T20:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421331-VariantEval-BETA 2020-01-07T21:00:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421351-CountReads 2020-01-07T20:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421371-FixVcfHeader-Picard 2020-01-07T20:58:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421391-CollectHsMetrics-Picard 2020-01-07T20:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421411-GnarlyGenotyper-BETA 2020-01-07T20:58:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421431-ViewSam-Picard 2020-01-07T21:00:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421451-CountVariants 2020-01-07T20:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421471-LiftOverIntervalList-Picard 2020-01-07T20:58:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421491-FilterSamReads-Picard 2020-01-07T20:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421511-PrimaryLineReadFilter 2020-01-07T20:59:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421531-CountBases 2020-01-07T20:57:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421551-CheckFingerprint-Picard 2020-01-07T20:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421571-DetermineGermlineContigPloidy-BETA 2020-01-07T20:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421591-FindBreakpointEvidenceSpark-BETA 2020-01-07T20:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421611-MappingQuality 2020-01-07T20:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421631-QualByDepth 2020-01-07T20:59:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421651-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T20:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421671-NormalizeFasta-Picard 2020-01-07T20:58:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421691-AS-RMSMappingQuality 2020-01-07T20:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421731-SamFormatConverter-Picard 2020-01-07T20:59:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421751-FisherStrand 2020-01-07T20:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421771-ClusterCrosscheckMetrics-Picard 2020-01-07T20:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421791-ClipReads 2020-01-07T20:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421811-CollectSamErrorMetrics-Picard 2020-01-07T20:57:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421831-MarkDuplicatesSpark-BETA 2020-01-07T20:58:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421851-DepthPerAlleleBySample 2020-01-07T20:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421871-SetNmMdAndUqTags-Picard 2020-01-07T20:59:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421891-CompareMetrics-Picard 2020-01-07T20:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421911-FuncotateSegments-BETA 2020-01-07T20:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421931-CalculateFingerprintMetrics-Picard 2020-01-07T20:56:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421951-AS-FisherStrand 2020-01-07T20:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421971-CompareBaseQualities 2020-01-07T20:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037421991-BwaSpark-BETA 2020-01-07T20:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422011-CollectAlignmentSummaryMetrics-Picard 2020-01-07T20:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422031-AnnotateVcfWithBamDepth 2020-01-07T20:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422051-CollectSequencingArtifactMetrics-Picard 2020-01-07T20:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422071-GatherVcfs-Picard 2020-01-07T20:58:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422091-ExtractSequences-Picard 2020-01-07T20:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422111-MarkDuplicatesWithMateCigar-Picard 2020-01-07T20:58:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422131-MakeSitesOnlyVcf-Picard 2020-01-07T20:58:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422151-CollectInsertSizeMetrics-Picard 2020-01-07T20:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422191-LeftAlignIndels 2020-01-07T20:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422231-MappingQualityRankSumTest 2020-01-07T20:58:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422251-MappingQualityNotZeroReadFilter 2020-01-07T20:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422271-HaplotypeCallerSpark-BETA 2020-01-07T20:58:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422311-NonNFastaSize-Picard 2020-01-07T20:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422331-FilterMutectCalls 2020-01-07T20:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422351-BaseRecalibratorSpark-BETA 2020-01-07T20:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422371-CollectQualityYieldMetricsSpark-BETA 2020-01-07T20:57:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422391-PlatformUnitReadFilter 2020-01-07T20:59:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422411-OxoGReadCounts 2020-01-07T20:59:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422431-PrintReads 2020-01-07T20:59:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422451-HaplotypeCaller 2020-01-07T20:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422471-ReadsPipelineSpark-BETA 2020-01-07T20:59:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422491-ReplaceSamHeader-Picard 2020-01-07T20:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422511-MateUnmappedAndUnmappedReadFilter 2020-01-07T20:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422531-CollectIlluminaLaneMetrics-Picard 2020-01-07T20:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422551-CountBasesInReference 2020-01-07T20:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422571-VcfToIntervalList-Picard 2020-01-07T21:00:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422591-MarkDuplicatesGATK-EXPERIMENTAL 2020-01-07T20:58:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422611-PathSeqBwaSpark 2020-01-07T20:59:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422631-MarkIlluminaAdapters-Picard 2020-01-07T20:58:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422651-SampleList 2020-01-07T20:59:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422671-FragmentLength 2020-01-07T20:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422691-CheckIlluminaDirectory-Picard 2020-01-07T20:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422711-CollectTargetedPcrMetrics-Picard 2020-01-07T20:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422731-MergeBamAlignment-Picard 2020-01-07T20:58:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422751-LeftAlignAndTrimVariants 2020-01-07T20:58:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422791-AmbiguousBaseReadFilter 2020-01-07T20:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422811-RemoveNearbyIndels 2020-01-07T20:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422831-CompareDuplicatesSpark-BETA 2020-01-07T20:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422851-FilterByOrientationBias-EXPERIMENTAL 2023-10-26T01:23:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422871-OriginalAlignment 2020-01-07T20:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422891-CreateSequenceDictionary-Picard 2020-01-07T20:57:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422911-VcfToAdpc-Picard 2020-01-07T21:00:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422931-GoodCigarReadFilter 2020-01-07T20:58:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422951-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T20:59:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422971-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T20:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037422991-PostprocessGermlineCNVCalls-BETA 2020-01-07T20:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423011-NotSupplementaryAlignmentReadFilter 2020-01-07T20:59:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423031-GenotypeSummaries 2020-01-24T13:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423051-FlagStatSpark-BETA 2020-01-07T20:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423071-CollectWgsMetrics-Picard 2020-01-07T20:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423091-FifoBuffer-Picard 2020-01-07T20:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423111-ExcessHet 2020-01-07T20:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423131-LikelihoodRankSumTest 2020-01-07T20:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423151-DownsampleSam-Picard 2020-01-07T20:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423171-CompareSAMs-Picard 2020-01-07T20:57:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423191-EstimateLibraryComplexityGATK-BETA 2020-01-07T20:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423231-DenoiseReadCounts-BETA 2020-01-07T20:57:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423251-BaseQualityRankSumTest 2020-01-07T20:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423271-IntervalListToBed-Picard 2020-01-07T20:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423291-ApplyVQSR 2020-01-07T20:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423311-GermlineCNVCaller-BETA 2020-01-07T20:58:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423331-ReadNameReadFilter 2020-01-07T20:59:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423351-CallCopyRatioSegments-BETA 2020-01-07T20:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423371-ScatterIntervalsByNs-Picard 2020-01-07T20:59:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423391-PlatformReadFilter 2020-01-07T20:59:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423411-BamIndexStats-Picard 2020-01-07T20:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423431-VcfFormatConverter-Picard 2020-01-07T21:00:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423451-AddOrReplaceReadGroups-Picard 2020-01-07T20:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423471-PlotModeledSegments-BETA 2020-01-07T20:59:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423491-LiftoverVcf-Picard 2020-01-07T20:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423511-ReadPosition 2020-01-07T20:59:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423531-MateOnSameContigOrNoMappedMateReadFilter 2020-01-07T20:58:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423551-ApplyBQSRSpark-BETA 2020-01-07T20:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423591-CalculateGenotypePosteriors 2020-01-07T20:56:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423611-CollectMultipleMetrics-Picard 2020-01-07T20:56:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423631-ValidateVariants 2020-01-07T21:00:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423651-ExtractSVEvidenceSpark-BETA 2020-01-07T20:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423671-CNNScoreVariants-EXPERIMENTAL 2020-01-07T20:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423691-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-01-07T20:59:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423711-CombineSegmentBreakpoints-EXPERIMENTAL 2020-01-07T20:57:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423731-FlagStat 2020-01-07T20:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423751-BaitDesigner-Picard 2020-01-07T20:56:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423771-InbreedingCoeff 2020-01-07T20:58:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423791-SortVcf-Picard 2020-01-07T20:59:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423831-PrintVariantsSpark-BETA 2020-01-07T20:59:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423851-ValidateSamFile-Picard 2020-01-07T21:00:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423871-FastqToSam-Picard 2020-01-07T20:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423891-SamToFastq-Picard 2020-01-07T20:59:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423911-SortSam-Picard 2020-01-07T20:59:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423931-CollectIlluminaBasecallingMetrics-Picard 2020-01-07T20:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423951-FuncotatorDataSourceDownloader-BETA 2020-01-07T20:58:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423971-StrandArtifact 2020-01-07T20:59:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037423991-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-01-07T20:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424011-CollectRnaSeqMetrics-Picard 2020-01-07T20:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424031-PassesVendorQualityCheckReadFilter 2020-01-07T20:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424051-AS-MappingQualityRankSumTest 2020-01-07T20:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424071-CollectFragmentCounts-BETA 2020-01-07T20:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424091-FixCallSetSampleOrdering-EXPERIMENTAL 2020-01-07T20:58:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424111-BaseQuality 2020-01-07T20:56:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424131-SeqIsStoredReadFilter 2020-01-07T20:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424151-PathSeqFilterSpark 2020-01-07T20:59:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424171-PlotDenoisedCopyRatios-BETA 2020-01-07T20:59:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424191-FastaAlternateReferenceMaker 2020-01-07T20:57:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424211-StructuralVariationDiscoveryPipelineSpark-BETA 2020-01-07T20:59:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424231-EvaluateInfoFieldConcordance-BETA 2020-01-07T20:57:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424251-CigarContainsNoNOperator 2020-01-07T20:56:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424271-SplitVcfs-Picard 2020-01-07T20:59:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424291-FilterFuncotations-EXPERIMENTAL 2020-01-07T20:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424311-SplitSamByLibrary-Picard 2020-01-07T20:59:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424331-CrosscheckFingerprints-Picard 2020-01-07T20:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424351-GenotypeGVCFs 2020-01-07T20:58:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424371-FindBadGenomicKmersSpark-BETA 2020-01-07T20:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424391-AS-QualByDepth 2020-01-07T20:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424411-Concordance-BETA 2020-01-07T20:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424431-FragmentLengthReadFilter 2020-01-07T20:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424451-CollectRrbsMetrics-Picard 2020-01-07T20:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424471-ValidAlignmentEndReadFilter 2020-01-07T21:00:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424491-DepthPerSampleHC 2020-01-07T20:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424511-AlleleFraction 2020-01-07T20:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424531-CountNs 2020-01-07T20:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424551-RenameSampleInVcf-Picard 2020-01-07T20:59:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424571-MappingQualityAvailableReadFilter 2020-01-07T20:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424591-CountReadsSpark-BETA 2020-01-07T20:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424611-PrintReadsSpark-BETA 2020-01-07T20:59:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424631-CreateSomaticPanelOfNormals-BETA 2020-01-07T20:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424651-CheckPileup 2020-01-07T20:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424671-GtcToVcf-Picard 2020-01-07T20:58:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424711-CheckTerminatorBlock-Picard 2020-01-07T20:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424731-CleanSam-Picard 2020-01-07T20:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037424991-CollectIndependentReplicateMetrics-Picard-BETA 2020-01-07T21:01:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425011-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2020-01-07T21:01:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425031-NonChimericOriginalAlignmentReadFilter 2020-01-07T21:03:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425051-MeanQualityByCycle-Picard 2020-01-07T21:02:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425071-CollectHiSeqXPfFailMetrics-Picard 2020-01-07T21:01:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425091-GenotypeConcordance-Picard 2020-01-07T21:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425111-WellformedReadFilter 2020-01-07T21:04:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425131-SampleReadFilter 2020-01-07T21:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425151-AnalyzeCovariates 2020-01-07T21:00:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425171-RMSMappingQuality 2020-01-07T21:03:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425191-FirstOfPairReadFilter 2020-01-07T21:02:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425311-CalcMetadataSpark-BETA 2020-01-07T21:00:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425331-AlignmentAgreesWithHeaderReadFilter 2020-01-07T21:00:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425351-AnnotatePairOrientation-BETA 2020-01-07T21:00:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425371-VariantEval-BETA 2020-01-07T21:04:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425391-FixVcfHeader-Picard 2020-01-07T21:02:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425411-GnarlyGenotyper-BETA 2020-01-07T21:02:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425431-EstimateLibraryComplexity-Picard 2020-01-07T21:01:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425451-ViewSam-Picard 2020-01-07T21:04:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425471-AnnotateVcfWithExpectedAlleleFraction 2020-01-07T21:00:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425491-FilterSamReads-Picard 2020-01-07T21:02:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425511-StrandOddsRatio 2020-01-07T21:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425531--Tool-Documentation-Index 2020-01-07T21:00:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425551-HasReadGroupReadFilter 2020-01-07T21:02:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425571-DetermineGermlineContigPloidy-BETA 2020-01-07T21:01:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425591-FindBreakpointEvidenceSpark-BETA 2020-01-07T21:02:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425631-MappingQuality 2020-01-07T21:02:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425651-QualByDepth 2020-01-07T21:03:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425671-NormalizeFasta-Picard 2020-01-07T21:03:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425691-CNNVariantWriteTensors-EXPERIMENTAL 2020-01-07T21:01:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425711-CountVariantsSpark-BETA 2020-01-07T21:01:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425731-UpdateVCFSequenceDictionary 2020-01-07T21:04:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425751-SamFormatConverter-Picard 2020-01-07T21:03:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425771-ClipReads 2020-01-07T21:01:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425791-CollectSamErrorMetrics-Picard 2020-01-07T21:01:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425811-SoftClippedReadFilter 2020-01-07T21:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425831-SortReadFileSpark-BETA 2020-01-07T21:03:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425851-SetNmMdAndUqTags-Picard 2020-01-07T21:03:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425871-FuncotateSegments-BETA 2020-01-07T21:02:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425891-BwaSpark-BETA 2020-01-07T21:00:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425911-CollectAlignmentSummaryMetrics-Picard 2020-01-07T21:01:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425931-GatherVcfs-Picard 2020-01-07T21:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425951-GatherBQSRReports 2020-01-07T21:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425971-CalculateContamination 2020-01-07T21:00:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037425991-PathSeqBuildKmers 2020-01-07T21:03:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426011-MakeSitesOnlyVcf-Picard 2020-01-07T21:02:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426031-StrandBiasBySample 2020-01-07T21:04:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426051-SortSamSpark-BETA 2020-01-07T21:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426071-FilterIntervals-BETA 2020-01-07T21:02:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426091-MappingQualityRankSumTest 2020-01-07T21:02:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426111-HaplotypeCallerSpark-BETA 2020-01-07T21:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426131-SplitSamByNumberOfReads-Picard 2020-01-07T21:04:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426151-BaseRecalibratorSpark-BETA 2020-01-07T21:00:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426171-IlluminaBasecallsToSam-Picard 2020-01-07T21:02:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426191-MappingQualityReadFilter 2020-01-07T21:02:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426211-PlatformUnitReadFilter 2020-01-07T21:03:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426231-OxoGReadCounts 2020-01-07T21:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426251-CreateHadoopBamSplittingIndex-BETA 2020-01-07T21:01:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426271-PrintReads 2020-01-07T21:03:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426291-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-01-07T21:00:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426311-ReadsPipelineSpark-BETA 2020-01-07T21:03:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426331-MateUnmappedAndUnmappedReadFilter 2020-01-07T21:02:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426351-CollectIlluminaLaneMetrics-Picard 2020-01-07T21:01:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426371-PolymorphicNuMT 2020-01-07T21:03:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426391-MarkDuplicatesGATK-EXPERIMENTAL 2020-01-07T21:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426411-MarkIlluminaAdapters-Picard 2020-01-07T21:02:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426431-MatchingBasesAndQualsReadFilter 2020-01-07T21:02:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426471-RevertSamSpark-BETA 2020-01-07T21:03:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426491-ExtractIlluminaBarcodes-Picard 2020-01-07T21:01:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426511-AmbiguousBaseReadFilter 2020-01-07T21:00:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426531-RemoveNearbyIndels 2020-01-07T21:03:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426551-CompareDuplicatesSpark-BETA 2020-01-07T21:01:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426571-FilterByOrientationBias-EXPERIMENTAL 2020-01-07T21:02:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426591-OriginalAlignment 2020-01-07T21:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426611-GoodCigarReadFilter 2020-01-07T21:02:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426631-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:02:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426651-ReorderSam-Picard 2020-01-07T21:03:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426671-CollectWgsMetrics-Picard 2020-01-07T21:01:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426691-PairedReadFilter 2020-01-07T21:03:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426711-AS-ReadPosRankSumTest 2020-01-07T21:00:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426731-GetPileupSummaries-BETA 2020-01-07T21:02:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426751-FifoBuffer-Picard 2020-01-07T21:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426771-ExcessHet 2020-01-07T21:01:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426791-VariantFiltration 2020-01-07T21:04:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426811-BaseRecalibrator 2020-01-07T21:00:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426851-ClippingRankSumTest 2020-01-07T21:01:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426871-BQSRPipelineSpark-BETA 2020-01-07T21:00:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426891-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:04:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426911-PossibleDeNovo 2020-01-07T21:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426931-CollectInsertSizeMetricsSpark-BETA 2020-01-07T21:01:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426951-DenoiseReadCounts-BETA 2020-01-07T21:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426971-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037426991-GermlineCNVCaller-BETA 2020-01-07T21:02:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427011-CallCopyRatioSegments-BETA 2020-01-07T21:00:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427031-PlatformReadFilter 2020-01-07T21:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427051-PlotModeledSegments-BETA 2020-01-07T21:03:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427071-CombineGVCFs 2020-01-07T21:01:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427091-CollectGcBiasMetrics-Picard 2020-01-07T21:01:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427111-ReadPosition 2020-01-07T21:03:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427131-MateOnSameContigOrNoMappedMateReadFilter 2020-01-07T21:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427151-ReadStrandFilter 2020-01-07T21:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427171-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-01-07T21:01:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427211-CalculateGenotypePosteriors 2020-01-07T21:00:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427231-MergeVcfs-Picard 2020-01-07T21:03:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427271-CollectAllelicCounts-BETA 2020-01-07T21:01:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427311-CNNScoreVariants-EXPERIMENTAL 2020-01-07T21:01:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427331-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-01-07T21:03:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427351-MethylationTypeCaller-EXPERIMENTAL 2020-01-07T21:03:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427371-PreprocessIntervals-BETA 2020-01-07T21:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427391-FlagStat 2020-01-07T21:02:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427411-BaitDesigner-Picard 2020-01-07T21:00:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427431-ReadLengthEqualsCigarLengthReadFilter 2020-01-07T21:03:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427451-PrintVariantsSpark-BETA 2020-01-07T21:03:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427471-ValidateSamFile-Picard 2020-01-07T21:04:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427491-SamToFastq-Picard 2020-01-07T21:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427511-CollectIlluminaBasecallingMetrics-Picard 2020-01-07T21:01:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427531-StrandArtifact 2020-01-07T21:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427551-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-01-07T21:01:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427571-MergeSamFiles-Picard 2020-01-07T21:03:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427611-GatherVcfsCloud-BETA 2020-01-07T21:02:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427631-AnnotateIntervals-BETA 2020-01-07T21:00:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427651-PassesVendorQualityCheckReadFilter 2020-01-07T21:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427671-SplitReads 2020-01-07T21:04:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427691-AS-MappingQualityRankSumTest 2020-01-07T21:00:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427711-CollectFragmentCounts-BETA 2020-01-07T21:01:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427731-BaseRecalibratorSparkSharded-EXPERIMENTAL 2020-01-07T21:00:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427751-ReadPosRankSumTest 2020-01-07T21:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427771-SeqIsStoredReadFilter 2020-01-07T21:03:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427791-IntervalOverlapReadFilter 2020-01-07T21:02:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427831-VariantRecalibrator 2020-01-07T21:04:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427851-SplitIntervals 2020-01-07T21:04:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427871-UnmarkDuplicates 2020-01-07T21:04:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427891-NonZeroFragmentLengthReadFilter 2020-01-07T21:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427911-ProperlyPairedReadFilter 2020-01-07T21:03:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427931-CigarContainsNoNOperator 2020-01-07T21:01:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427951-SplitVcfs-Picard 2020-01-07T21:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427971-CNNVariantTrain-EXPERIMENTAL 2020-01-07T21:01:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037427991-TandemRepeat 2020-01-07T21:04:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428011-AddCommentsToBam-Picard 2020-01-07T21:00:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428031-AS-BaseQualityRankSumTest 2020-01-07T21:00:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428051-Concordance-BETA 2020-01-07T21:01:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428071-FragmentLengthReadFilter 2020-01-07T21:02:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428091-FindMendelianViolations-Picard 2020-01-07T21:02:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428111-IndexFeatureFile 2023-08-13T01:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428131-MetricsReadFilter 2020-01-07T21:03:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428151-QualityScoreDistributionSpark-BETA 2020-01-07T21:03:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428171-OrientationBiasReadCounts 2020-01-07T21:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428191-CountNs 2020-01-07T21:01:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428211-MappingQualityAvailableReadFilter 2020-01-07T21:02:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428231-CollectOxoGMetrics-Picard 2020-01-07T21:01:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428251-CountBasesSpark-BETA 2020-01-07T21:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428271-PrintReadsSpark-BETA 2020-01-07T21:03:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428291-ASEReadCounter 2020-01-07T21:00:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428311-FilterVariantTranches-EXPERIMENTAL 2020-01-07T21:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428331-ReadLengthReadFilter 2020-01-07T21:03:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428351-CleanSam-Picard 2020-01-07T21:01:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428551-CollectIndependentReplicateMetrics-Picard-BETA 2020-01-07T21:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428571-ChromosomeCounts 2020-01-07T21:05:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428591-LibraryReadFilter 2020-01-07T21:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428611-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2020-01-07T21:05:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428631-NonChimericOriginalAlignmentReadFilter 2020-01-07T21:07:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428651-CollectHiSeqXPfFailMetrics-Picard 2020-01-07T21:05:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428671-AnalyzeCovariates 2020-01-07T21:04:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428691-FirstOfPairReadFilter 2020-01-07T21:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428711-Funcotator-BETA 2020-01-07T21:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428731-CollectQualityYieldMetrics-Picard 2020-01-07T21:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428751-PathSeqPipelineSpark 2020-01-07T21:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428771-AS-StrandOddsRatio 2020-01-07T21:04:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428791-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-01-07T21:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428811-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428831-CountReads 2020-01-07T21:05:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428851-FixVcfHeader-Picard 2020-01-07T21:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428871-CollectHsMetrics-Picard 2020-01-07T21:05:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428891-EstimateLibraryComplexity-Picard 2020-01-07T21:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428911-AnnotateVcfWithExpectedAlleleFraction 2020-01-07T21:04:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428931-NotDuplicateReadFilter 2020-01-07T21:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428951-BamToBfq-Picard 2020-01-07T21:04:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428971-VariantAnnotator-BETA 2020-01-07T21:08:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037428991-PrimaryLineReadFilter 2020-01-07T21:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429011-CountBases 2020-01-07T21:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429031-StrandOddsRatio 2020-01-07T21:08:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429051--Tool-Documentation-Index 2020-01-07T21:04:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429071-CheckFingerprint-Picard 2020-01-07T21:05:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429091-HasReadGroupReadFilter 2020-01-07T21:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429111-FindBreakpointEvidenceSpark-BETA 2020-01-07T21:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429131-UniqueAltReadCount 2020-01-07T21:08:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429151-MappingQuality 2020-01-07T21:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429171-VariantsToTable 2020-01-07T21:08:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429211-NormalizeFasta-Picard 2020-01-07T21:07:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429231-CNNVariantWriteTensors-EXPERIMENTAL 2020-01-07T21:05:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429251-UpdateVCFSequenceDictionary 2020-01-07T21:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429271-IlluminaBasecallsToFastq-Picard 2020-01-07T21:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429291-ClipReads 2020-01-07T21:05:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429311-CollectSamErrorMetrics-Picard 2020-01-07T21:05:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429331-SoftClippedReadFilter 2020-01-07T21:08:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429351-MarkDuplicatesSpark-BETA 2020-01-07T21:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429371-CalculateReadGroupChecksum-Picard 2020-01-07T21:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429391-SetNmMdAndUqTags-Picard 2020-01-07T21:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429411-CalculateFingerprintMetrics-Picard 2020-01-07T21:05:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429431-AS-FisherStrand 2020-01-07T21:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429451-CompareBaseQualities 2020-01-07T21:05:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429471-AnnotateVcfWithBamDepth 2020-01-07T21:04:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429491-CollectSequencingArtifactMetrics-Picard 2020-01-07T21:05:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429511-MappedReadFilter 2020-01-07T21:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429531-MarkDuplicatesWithMateCigar-Picard 2020-01-07T21:07:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429551-GatherBQSRReports 2020-01-07T21:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429571-CpxVariantReInterpreterSpark-BETA 2020-01-07T21:06:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429591-PathSeqBuildKmers 2020-01-07T21:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429611-CollectInsertSizeMetrics-Picard 2020-01-07T21:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429631-SortSamSpark-BETA 2020-01-07T21:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429651-LeftAlignIndels 2020-01-07T21:07:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429671-MateDifferentStrandReadFilter 2020-01-07T21:07:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429691-NonNFastaSize-Picard 2020-01-07T21:07:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429711-FilterMutectCalls 2020-01-07T21:06:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429731-BaseRecalibratorSpark-BETA 2020-01-07T21:04:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429751-SelectVariants 2020-01-07T21:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429791-IlluminaBasecallsToSam-Picard 2020-01-07T21:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429811-CollectQualityYieldMetricsSpark-BETA 2020-01-07T21:05:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429851-PrintReads 2020-01-07T21:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429871-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-01-07T21:05:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429891-MateUnmappedAndUnmappedReadFilter 2020-01-07T21:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429911-CollectIlluminaLaneMetrics-Picard 2020-01-07T21:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429931-CountBasesInReference 2020-01-07T21:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429951-VcfToIntervalList-Picard 2020-01-07T21:08:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429971-SetNmAndUqTags-Picard 2020-01-07T21:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037429991-MeanQualityByCycleSpark-BETA 2020-01-07T21:07:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430011-CheckIlluminaDirectory-Picard 2020-01-07T21:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430031-CollectTargetedPcrMetrics-Picard 2020-01-07T21:05:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430051-ReblockGVCF-EXPERIMENTAL 2020-01-07T21:08:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430071-FixMisencodedBaseQualityReads 2020-01-07T21:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430091-AmbiguousBaseReadFilter 2020-01-07T21:04:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430111-CompareDuplicatesSpark-BETA 2020-01-07T21:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430131-CollectRawWgsMetrics-Picard 2020-01-07T21:05:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430151-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-01-07T21:08:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430171-GoodCigarReadFilter 2020-01-07T21:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430191-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430211-PositionBasedDownsampleSam-Picard 2020-01-07T21:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430231-FlagStatSpark-BETA 2020-01-07T21:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430251-CollectWgsMetrics-Picard 2020-01-07T21:05:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430271-AS-ReadPosRankSumTest 2020-01-07T21:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430291-FifoBuffer-Picard 2020-01-07T21:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430311-VariantFiltration 2020-01-07T21:08:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430331-BaseRecalibrator 2020-01-07T21:04:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430351-RevertBaseQualityScores 2020-01-07T21:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430371-GatherTranches-BETA 2020-01-07T21:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430411-PossibleDeNovo 2020-01-07T21:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430431-DenoiseReadCounts-BETA 2020-01-07T21:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430451-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430471-IntervalListToBed-Picard 2020-01-07T21:07:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430491-ApplyVQSR 2020-01-07T21:04:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430511-GermlineCNVCaller-BETA 2020-01-07T21:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430531-UpdateVcfSequenceDictionary-Picard 2020-01-07T21:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430551-ReadNameReadFilter 2020-01-07T21:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430571-MappingQualityZero 2020-01-07T21:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430591-ScatterIntervalsByNs-Picard 2020-01-07T21:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430611-PlatformReadFilter 2020-01-07T21:07:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430631-Mutect2 2020-01-07T21:07:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430651-AddOrReplaceReadGroups-Picard 2020-01-07T21:04:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430671-PlotModeledSegments-BETA 2020-01-07T21:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430691-CombineGVCFs 2020-01-07T21:05:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430711-CollectGcBiasMetrics-Picard 2020-01-07T21:05:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430731-ReadPosition 2020-01-07T21:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430751-MateOnSameContigOrNoMappedMateReadFilter 2020-01-07T21:07:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430771-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-01-07T21:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430791-CalculateGenotypePosteriors 2020-01-07T21:05:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430811-MergeVcfs-Picard 2020-01-07T21:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430851-ValidateVariants 2020-01-07T21:08:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430871-ExtractSVEvidenceSpark-BETA 2020-01-07T21:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430891-PreprocessIntervals-BETA 2020-01-07T21:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430911-QualityScoreDistribution-Picard 2020-01-07T21:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430931-CombineSegmentBreakpoints-EXPERIMENTAL 2020-01-07T21:05:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430951-BaitDesigner-Picard 2020-01-07T21:04:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430971-ReadLengthEqualsCigarLengthReadFilter 2020-01-07T21:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037430991-SortVcf-Picard 2020-01-07T21:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431011-PrintVariantsSpark-BETA 2020-01-07T21:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431031-FastqToSam-Picard 2020-01-07T21:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431051-SamToFastq-Picard 2020-01-07T21:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431071-CollectIlluminaBasecallingMetrics-Picard 2020-01-07T21:05:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431091-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-01-07T21:05:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431111-GatherVcfsCloud-BETA 2020-01-07T21:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431131-AnnotateIntervals-BETA 2020-01-07T21:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431151-SplitReads 2020-01-07T21:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431171-FixCallSetSampleOrdering-EXPERIMENTAL 2020-01-07T21:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431211-ReadPosRankSumTest 2020-01-07T21:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431231-BaseQuality 2020-01-07T21:04:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431251-IntervalOverlapReadFilter 2020-01-07T21:07:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431271-NonZeroReferenceLengthAlignmentReadFilter 2020-01-07T21:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431291-VariantRecalibrator 2020-01-07T21:08:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431311-PathSeqFilterSpark 2020-01-07T21:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431331-PlotDenoisedCopyRatios-BETA 2020-01-07T21:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431351-SplitIntervals 2020-01-07T21:08:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431371-UnmarkDuplicates 2020-01-07T21:08:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431391-SplitNCigarReads 2020-01-07T21:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431411-NonZeroFragmentLengthReadFilter 2020-01-07T21:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431431-CigarContainsNoNOperator 2020-01-07T21:05:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431451-SplitVcfs-Picard 2020-01-07T21:08:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431471-CrosscheckFingerprints-Picard 2020-01-07T21:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431491-CNNVariantTrain-EXPERIMENTAL 2020-01-07T21:05:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431511-GenotypeGVCFs 2020-01-07T21:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431531-TandemRepeat 2020-01-07T21:08:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431551-AddCommentsToBam-Picard 2020-01-07T21:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431571-Concordance-BETA 2020-01-07T21:05:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431591-BuildBamIndex-Picard 2020-01-07T21:05:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431611-IndexFeatureFile 2020-01-07T21:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431631-ValidAlignmentEndReadFilter 2020-01-07T21:08:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431651-AlleleFraction 2020-01-07T21:04:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431671-CountNs 2020-01-07T21:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431691-RenameSampleInVcf-Picard 2020-01-07T21:08:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431711-MappingQualityAvailableReadFilter 2020-01-07T21:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431731-CreateReadCountPanelOfNormals-BETA 2020-01-07T21:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431751-CountReadsSpark-BETA 2020-01-07T21:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431791-ASEReadCounter 2020-01-07T21:04:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431811-FilterVariantTranches-EXPERIMENTAL 2020-01-07T21:06:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431831-CheckPileup 2020-01-07T21:05:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037431851-GtcToVcf-Picard 2020-01-07T21:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037432931-ChromosomeCounts 2020-01-07T21:09:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037432951-CollectWgsMetricsWithNonZeroCoverage-Picard-BETA 2020-01-07T21:10:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037432971-NonChimericOriginalAlignmentReadFilter 2020-01-07T21:11:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037432991-GenotypeConcordance-Picard 2020-01-07T21:11:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433011-Pileup 2020-01-07T21:12:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433031-RMSMappingQuality 2020-01-07T21:12:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433051-Funcotator-BETA 2020-01-07T21:11:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433111-SecondOfPairReadFilter 2020-01-07T21:12:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433131-FilterVcf-Picard 2020-01-07T21:10:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433151-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-01-07T21:12:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433171-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:12:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433191-AnnotateVcfWithExpectedAlleleFraction 2020-01-07T21:09:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433211-LiftOverIntervalList-Picard 2020-01-07T21:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433231-NotDuplicateReadFilter 2020-01-07T21:11:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433251-BamToBfq-Picard 2020-01-07T21:09:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433271-VariantAnnotator-BETA 2020-01-07T21:13:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433311-FilterSamReads-Picard 2020-01-07T21:10:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433331-PrimaryLineReadFilter 2020-01-07T21:12:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433351-CollectMultipleMetricsSpark-BETA 2020-01-07T21:09:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433371-StrandOddsRatio 2020-01-07T21:12:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433391--Tool-Documentation-Index 2020-01-07T21:09:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433411-CheckFingerprint-Picard 2020-01-07T21:09:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433431-HasReadGroupReadFilter 2020-01-07T21:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433451-UniqueAltReadCount 2020-01-07T21:12:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433471-CNNVariantWriteTensors-EXPERIMENTAL 2020-01-07T21:09:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433491-CountVariantsSpark-BETA 2020-01-07T21:10:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433511-UpdateVCFSequenceDictionary 2020-01-07T21:13:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433531-SamFormatConverter-Picard 2020-01-07T21:12:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433551-FisherStrand 2020-01-07T21:10:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433571-CollectSamErrorMetrics-Picard 2020-01-07T21:10:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433591-SortReadFileSpark-BETA 2020-01-07T21:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433611-SetNmMdAndUqTags-Picard 2020-01-07T21:12:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433631-CompareMetrics-Picard 2020-01-07T21:10:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433651-AS-FisherStrand 2020-01-07T21:09:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433671-CompareBaseQualities 2020-01-07T21:10:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433691-BwaSpark-BETA 2020-01-07T21:09:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433711-CollectSequencingArtifactMetrics-Picard 2020-01-07T21:10:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433731-MappedReadFilter 2020-01-07T21:11:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433751-ExtractSequences-Picard 2020-01-07T21:10:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433771-GatherBQSRReports 2020-01-07T21:11:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433791-CalculateContamination 2020-01-07T21:09:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433811-CpxVariantReInterpreterSpark-BETA 2020-01-07T21:10:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433831-MakeSitesOnlyVcf-Picard 2020-01-07T21:11:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433851-IntervalListTools-Picard 2020-01-07T21:11:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433871-StrandBiasBySample 2020-01-07T21:12:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433891-SortSamSpark-BETA 2020-01-07T21:12:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433911-MappingQualityRankSumTest 2020-01-07T21:11:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433931-HaplotypeCallerSpark-BETA 2020-01-07T21:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433951-CollectJumpingLibraryMetrics-Picard 2020-01-07T21:09:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433971-NonNFastaSize-Picard 2020-01-07T21:11:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037433991-CalculateMixingFractions 2020-01-07T21:09:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434011-SelectVariants 2020-01-07T21:12:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434031-IlluminaBasecallsToSam-Picard 2020-01-07T21:11:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434051-ReadGroupReadFilter 2020-01-07T21:12:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434071-MappingQualityReadFilter 2020-01-07T21:11:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434091-PlatformUnitReadFilter 2020-01-07T21:12:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434111-OxoGReadCounts 2020-01-07T21:11:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434131-CrosscheckReadGroupFingerprints-Picard 2020-01-07T21:10:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434151-ReadsPipelineSpark-BETA 2020-01-07T21:12:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434171-ReplaceSamHeader-Picard 2020-01-07T21:12:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434191-MateUnmappedAndUnmappedReadFilter 2020-01-07T21:11:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434211-CollectIlluminaLaneMetrics-Picard 2020-01-07T21:09:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434231-CountBasesInReference 2020-01-07T21:10:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434251-SetNmAndUqTags-Picard 2020-01-07T21:12:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434271-PathSeqBwaSpark 2020-01-07T21:12:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434291-MarkIlluminaAdapters-Picard 2020-01-07T21:11:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434311-MeanQualityByCycleSpark-BETA 2020-01-07T21:11:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434331-CheckIlluminaDirectory-Picard 2020-01-07T21:09:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434351-CollectBaseDistributionByCycle-Picard 2020-01-07T21:09:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434371-MergeBamAlignment-Picard 2020-01-07T21:11:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434391-RemoveNearbyIndels 2020-01-07T21:12:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434411-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-01-07T21:13:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434431-MarkDuplicates-Picard 2020-01-07T21:11:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434451-GoodCigarReadFilter 2020-01-07T21:11:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434471-SimpleMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:12:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434491-PositionBasedDownsampleSam-Picard 2020-01-07T21:12:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434511-PostprocessGermlineCNVCalls-BETA 2020-01-07T21:12:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434531-NotSupplementaryAlignmentReadFilter 2020-01-07T21:11:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434551-GenotypeSummaries 2020-01-07T21:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434591-FilterAlignmentArtifacts-EXPERIMENTAL 2020-01-07T21:10:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434611-CollectWgsMetrics-Picard 2020-01-07T21:10:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434631-AS-ReadPosRankSumTest 2020-01-07T21:09:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434651-GetPileupSummaries-BETA 2020-01-07T21:11:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434671-ExcessHet 2020-01-07T21:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration 2020-01-07T21:13:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434711-LikelihoodRankSumTest 2020-01-07T21:11:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434731-ClippingRankSumTest 2020-01-07T21:09:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434771-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-01-07T21:12:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434791-IntervalListToBed-Picard 2020-01-07T21:11:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434811-ApplyVQSR 2020-01-07T21:09:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434851-CallCopyRatioSegments-BETA 2020-01-07T21:09:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434871-PlatformReadFilter 2020-01-07T21:12:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434891-BamIndexStats-Picard 2020-01-07T21:09:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434911-VcfFormatConverter-Picard 2020-01-07T21:13:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434931-AddOrReplaceReadGroups-Picard 2020-01-07T21:09:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434951-PlotModeledSegments-BETA 2020-01-07T21:12:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434971-CombineGVCFs 2020-01-07T21:10:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037434991-LiftoverVcf-Picard 2020-01-07T21:11:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435011-ReadStrandFilter 2020-01-07T21:12:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435031-ApplyBQSRSpark-BETA 2020-01-07T21:09:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435051-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-01-07T21:10:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435071-MergeVcfs-Picard 2020-01-07T21:11:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435091-ValidateVariants 2020-01-07T21:13:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435111-CNNScoreVariants-EXPERIMENTAL 2020-01-07T21:09:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435131-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-01-07T21:12:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435151-PreprocessIntervals-BETA 2020-01-07T21:12:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435171-CombineSegmentBreakpoints-EXPERIMENTAL 2020-01-07T21:10:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435191-FlagStat 2020-01-07T21:10:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435211-InbreedingCoeff 2020-01-07T21:11:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435231-ReadLengthEqualsCigarLengthReadFilter 2020-01-07T21:12:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435251-FixMateInformation-Picard 2020-01-07T21:10:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435271-SortVcf-Picard 2020-01-07T21:12:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435291-FastqToSam-Picard 2020-01-07T21:10:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435311-ReadGroupBlackListReadFilter 2020-01-07T21:12:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435331-SamToFastq-Picard 2020-01-07T21:12:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435351-SortSam-Picard 2020-01-07T21:12:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435371-CollectIlluminaBasecallingMetrics-Picard 2020-01-07T21:09:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435391-MergeSamFiles-Picard 2020-01-07T21:11:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435411-PathSeqScoreSpark 2020-01-07T21:12:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435431-RevertSam-Picard 2020-01-07T21:12:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435451-AS-MappingQualityRankSumTest 2020-01-07T21:09:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435471-FixCallSetSampleOrdering-EXPERIMENTAL 2020-01-07T21:10:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435491-BaseQuality 2020-01-07T21:09:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435511-SeqIsStoredReadFilter 2020-01-07T21:12:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435531-IntervalOverlapReadFilter 2020-01-07T21:11:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435551-NonZeroReferenceLengthAlignmentReadFilter 2020-01-07T21:11:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435611-PathSeqFilterSpark 2020-01-07T21:12:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435631-PlotDenoisedCopyRatios-BETA 2020-01-07T21:12:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435651-FastaAlternateReferenceMaker 2020-01-07T21:10:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435671-StructuralVariationDiscoveryPipelineSpark-BETA 2020-01-07T21:12:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435691-EvaluateInfoFieldConcordance-BETA 2020-01-07T21:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435711-SplitNCigarReads 2020-01-07T21:12:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435731-NonZeroFragmentLengthReadFilter 2020-01-07T21:11:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435751-CigarContainsNoNOperator 2020-01-07T21:09:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435771-SplitVcfs-Picard 2020-01-07T21:12:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435791-FilterFuncotations-EXPERIMENTAL 2020-01-07T21:10:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435811-CrosscheckFingerprints-Picard 2020-01-07T21:10:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435831-GenotypeGVCFs 2020-01-07T21:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435851-TandemRepeat 2020-01-07T21:12:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435871-AddCommentsToBam-Picard 2020-01-07T21:09:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435891-AnalyzeSaturationMutagenesis-BETA 2020-01-07T21:09:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435911-AS-QualByDepth 2020-01-07T21:09:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435931-AS-BaseQualityRankSumTest 2020-01-07T21:09:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435951-BuildBamIndex-Picard 2020-01-07T21:09:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435971-FindMendelianViolations-Picard 2020-01-07T21:10:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037435991-ReferenceBases 2020-01-07T21:12:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436011-ValidAlignmentEndReadFilter 2020-01-07T21:13:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436031-DepthPerSampleHC 2020-01-07T21:10:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436051-OrientationBiasReadCounts 2020-01-07T21:11:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436071-MappingQualityAvailableReadFilter 2020-01-07T21:11:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436091-CreateReadCountPanelOfNormals-BETA 2020-01-07T21:10:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436111-CountReadsSpark-BETA 2020-01-07T21:10:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436131-CountBasesSpark-BETA 2020-01-07T21:10:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436151-ASEReadCounter 2020-01-07T21:09:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436171-FilterVariantTranches-EXPERIMENTAL 2020-01-07T21:10:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436191-CheckPileup 2020-01-07T21:09:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436211-CleanSam-Picard 2020-01-07T21:09:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436471-CollectIndependentReplicateMetrics-Picard-BETA 2020-01-07T21:14:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436491-ChromosomeCounts 2020-01-07T21:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436511-LibraryReadFilter 2020-01-07T21:15:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436531-NonChimericOriginalAlignmentReadFilter 2020-01-07T21:16:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436551-CollectHiSeqXPfFailMetrics-Picard 2020-01-07T21:14:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436571-GenotypeConcordance-Picard 2020-01-07T21:15:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436591-BwaMemIndexImageCreator 2020-01-07T21:13:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436611-SampleReadFilter 2020-01-07T21:16:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436631-FirstOfPairReadFilter 2020-01-07T21:15:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436651-PathSeqPipelineSpark 2020-01-07T21:16:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436671-CalcMetadataSpark-BETA 2020-01-07T21:13:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436691-SecondOfPairReadFilter 2020-01-07T21:16:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436711-AnnotatePairOrientation-BETA 2020-01-07T21:13:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436731-VariantEval-BETA 2020-01-07T21:17:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436751-CountReads 2020-01-07T21:14:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436771-CollectHsMetrics-Picard 2020-01-07T21:14:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436791-GnarlyGenotyper-BETA 2020-01-07T21:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436811-EstimateLibraryComplexity-Picard 2020-01-07T21:14:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436831-ViewSam-Picard 2020-01-07T21:17:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436851-AnnotateVcfWithExpectedAlleleFraction 2020-01-07T21:13:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436871-VariantAnnotator-BETA 2020-01-07T21:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436891-FilterSamReads-Picard 2020-01-07T21:15:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436911-PrimaryLineReadFilter 2020-01-07T21:16:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436931-CollectMultipleMetricsSpark-BETA 2020-01-07T21:14:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436951-CountBases 2020-01-07T21:14:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436971-StrandOddsRatio 2020-01-07T21:17:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037436991--Tool-Documentation-Index 2020-01-07T21:13:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437011-CheckFingerprint-Picard 2020-01-07T21:13:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437031-HasReadGroupReadFilter 2020-01-07T21:15:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437051-DetermineGermlineContigPloidy-BETA 2020-01-07T21:14:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437071-FilterLongReadAlignmentsSAMSpark-EXPERIMENTAL 2020-01-07T21:15:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437091-AS-RMSMappingQuality 2020-01-07T21:13:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437111-IlluminaBasecallsToFastq-Picard 2020-01-07T21:15:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437131-SamFormatConverter-Picard 2020-01-07T21:16:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437151-ClusterCrosscheckMetrics-Picard 2020-01-07T21:13:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437171-CollectSamErrorMetrics-Picard 2020-01-07T21:14:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437191-GetSampleName-BETA 2020-01-07T21:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437211-MarkDuplicatesSpark-BETA 2020-01-07T21:15:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437231-DepthPerAlleleBySample 2020-01-07T21:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437251-SortReadFileSpark-BETA 2020-01-07T21:17:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437271-GatherBamFiles-Picard 2020-01-07T21:15:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437291-PathSeqBuildReferenceTaxonomy 2020-01-07T21:16:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437311-AS-FisherStrand 2020-01-07T21:13:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437331-BwaSpark-BETA 2020-01-07T21:13:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437351-MappedReadFilter 2020-01-07T21:15:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437371-MarkDuplicatesWithMateCigar-Picard 2020-01-07T21:15:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437391-GatherBQSRReports 2020-01-07T21:15:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437411-CalculateContamination 2020-01-07T21:13:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437431-ApplyBQSR 2020-01-07T21:13:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437451-PathSeqBuildKmers 2020-01-07T21:16:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437571-CollectInsertSizeMetrics-Picard 2020-01-07T21:14:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437591-StrandBiasBySample 2020-01-07T21:17:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437611-CollectReadCounts-BETA 2020-01-07T21:14:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437631-SortSamSpark-BETA 2020-01-07T21:17:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437651-MappingQualityRankSumTest 2020-01-07T21:15:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437671-HaplotypeCallerSpark-BETA 2020-01-07T21:15:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437691-CollectJumpingLibraryMetrics-Picard 2020-01-07T21:14:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437711-SplitSamByNumberOfReads-Picard 2020-01-07T21:17:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437731-MateDifferentStrandReadFilter 2020-01-07T21:15:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437751-CalculateMixingFractions 2020-01-07T21:13:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437771-IlluminaBasecallsToSam-Picard 2020-01-07T21:15:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437791-MappingQualityReadFilter 2020-01-07T21:15:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437811-GenomicsDBImport 2020-01-07T21:15:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437831-PlatformUnitReadFilter 2020-01-07T21:16:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437851-OxoGReadCounts 2020-01-07T21:16:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437871-PrintReads 2020-01-07T21:16:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437891-CrosscheckReadGroupFingerprints-Picard 2020-01-07T21:14:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437911-ValidAlignmentStartReadFilter 2020-01-07T21:17:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437931-ReadsPipelineSpark-BETA 2020-01-07T21:16:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437951-CountFalsePositives-BETA 2020-01-07T21:14:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437971-MateUnmappedAndUnmappedReadFilter 2020-01-07T21:16:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037437991-CountBasesInReference 2020-01-07T21:14:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438011-VcfToIntervalList-Picard 2020-01-07T21:17:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438031-MarkIlluminaAdapters-Picard 2020-01-07T21:15:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438051-SampleList 2020-01-07T21:16:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438071-MatchingBasesAndQualsReadFilter 2020-01-07T21:15:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438091-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-01-07T21:14:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438111-CheckIlluminaDirectory-Picard 2020-01-07T21:13:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438131-CollectTargetedPcrMetrics-Picard 2020-01-07T21:14:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438151-MergeBamAlignment-Picard 2020-01-07T21:16:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438171-ModelSegments-BETA 2020-01-07T21:16:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438191-RevertSamSpark-BETA 2020-01-07T21:16:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438211-ExtractIlluminaBarcodes-Picard 2020-01-07T21:14:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438231-AmbiguousBaseReadFilter 2020-01-07T21:13:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438251-RemoveNearbyIndels 2020-01-07T21:16:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438271-CollectRawWgsMetrics-Picard 2020-01-07T21:14:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438291-FilterByOrientationBias-EXPERIMENTAL 2020-01-07T21:15:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438311-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-01-07T21:17:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438351-MarkDuplicates-Picard 2020-01-07T21:15:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438371-VcfToAdpc-Picard 2020-01-07T21:17:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438391-PositionBasedDownsampleSam-Picard 2020-01-07T21:16:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438411-ReorderSam-Picard 2020-01-07T21:16:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438431-FilterAlignmentArtifacts-EXPERIMENTAL 2020-01-07T21:14:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438471-VariantFiltration 2020-01-07T21:17:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438491-BaseRecalibrator 2020-01-07T21:13:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438511-RevertBaseQualityScores 2020-01-07T21:16:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438531-GatherTranches-BETA 2020-01-07T21:15:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438551-ClippingRankSumTest 2020-01-07T21:13:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438571-EstimateLibraryComplexityGATK-BETA 2020-01-07T21:14:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438591-UmiAwareMarkDuplicatesWithMateCigar-Picard-BETA 2020-01-07T21:17:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438611-DenoiseReadCounts-BETA 2020-01-07T21:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438631-BaseQualityRankSumTest 2020-01-07T21:13:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438651-GermlineCNVCaller-BETA 2020-01-07T21:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438671-ReadNameReadFilter 2020-01-07T21:16:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438691-MappingQualityZero 2020-01-07T21:15:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438711-CallCopyRatioSegments-BETA 2020-01-07T21:13:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438731-PlatformReadFilter 2020-01-07T21:16:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438751-BamIndexStats-Picard 2020-01-07T21:13:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438771-FilterMutectCalls 2020-01-07T21:15:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438791-Mutect2 2020-01-07T21:16:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438811-AddOrReplaceReadGroups-Picard 2020-01-07T21:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438831-PlotModeledSegments-BETA 2020-01-07T21:16:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438871-CombineGVCFs 2020-01-07T21:14:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438891-LiftoverVcf-Picard 2020-01-07T21:15:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438911-AddOATag-Picard 2020-01-07T21:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438931-ApplyBQSRSpark-BETA 2020-01-07T21:13:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438951-MergeVcfs-Picard 2020-01-07T21:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438971-CollectMultipleMetrics-Picard 2020-01-07T21:14:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037438991-CollectAllelicCounts-BETA 2020-01-07T21:14:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439011-PreprocessIntervals-BETA 2020-01-07T21:16:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439031-QualityScoreDistribution-Picard 2020-01-07T21:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439051-FixMateInformation-Picard 2020-01-07T21:15:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439071-SortVcf-Picard 2020-01-07T21:17:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439091-SamToFastq-Picard 2020-01-07T21:16:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439111-SortSam-Picard 2020-01-07T21:17:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439131-CollectIlluminaBasecallingMetrics-Picard 2020-01-07T21:14:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439171-FuncotatorDataSourceDownloader-BETA 2020-01-07T21:15:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439191-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-01-07T21:14:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439211-MergeSamFiles-Picard 2020-01-07T21:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439231-PathSeqScoreSpark 2020-01-07T21:16:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439251-PassesVendorQualityCheckReadFilter 2020-01-07T21:16:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439271-SplitReads 2020-01-07T21:17:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439291-CollectFragmentCounts-BETA 2020-01-07T21:14:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439311-FixCallSetSampleOrdering-EXPERIMENTAL 2020-01-07T21:15:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439331-ReadPosRankSumTest 2020-01-07T21:16:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439351-BaseQuality 2020-01-07T21:13:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439371-IntervalOverlapReadFilter 2020-01-07T21:15:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439391-PathSeqFilterSpark 2020-01-07T21:16:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439411-SplitIntervals 2020-01-07T21:17:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439431-FastaAlternateReferenceMaker 2020-01-07T21:14:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439451-StructuralVariationDiscoveryPipelineSpark-BETA 2020-01-07T21:17:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439471-EvaluateInfoFieldConcordance-BETA 2020-01-07T21:14:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439491-NonZeroFragmentLengthReadFilter 2020-01-07T21:16:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439511-PileupSpark-BETA 2020-01-07T21:16:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439531-ProperlyPairedReadFilter 2020-01-07T21:16:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439551-CigarContainsNoNOperator 2020-01-07T21:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439571-SplitVcfs-Picard 2020-01-07T21:17:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439591-SplitSamByLibrary-Picard 2020-01-07T21:17:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439611-CrosscheckFingerprints-Picard 2020-01-07T21:14:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439631-GenotypeGVCFs 2020-01-07T21:15:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439651-FindBadGenomicKmersSpark-BETA 2020-01-07T21:15:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439691-AS-BaseQualityRankSumTest 2020-01-07T21:13:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439711-NotSecondaryAlignmentReadFilter 2020-01-07T21:16:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439731-FindMendelianViolations-Picard 2020-01-07T21:15:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439751-ValidAlignmentEndReadFilter 2020-01-07T21:17:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439771-FastaReferenceMaker 2020-01-07T21:14:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439791-AlleleFraction 2020-01-07T21:13:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439811-OrientationBiasReadCounts 2020-01-07T21:16:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439831-CountNs 2020-01-07T21:14:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439851-CountReadsSpark-BETA 2020-01-07T21:14:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439871-FilterVariantTranches-EXPERIMENTAL 2020-01-07T21:15:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439891-CreateSomaticPanelOfNormals-BETA 2020-01-07T21:14:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439911-CheckPileup 2020-01-07T21:13:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439931-GtcToVcf-Picard 2020-01-07T21:15:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439951-CheckTerminatorBlock-Picard 2020-01-07T21:13:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439971-ReadLengthReadFilter 2020-01-07T21:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037439991-CleanSam-Picard 2020-01-07T21:13:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38 2025-01-22T08:03:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037499012-I-am-unable-to-use-VQSR-recalibration-to-filter-variants 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591511-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2019-12-05T15:05:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591531-ChromosomeCounts 2019-12-05T15:05:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591551-LibraryReadFilter 2019-12-05T15:05:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591571-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2019-12-05T15:10:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591591-NonChimericOriginalAlignmentReadFilter 2019-12-05T15:05:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591611-GenotypeConcordance-Picard 2019-12-05T15:10:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591631-Pileup 2019-12-05T15:10:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591651-OverclippedReadFilter 2019-12-05T15:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591671-BwaMemIndexImageCreator 2019-12-05T15:10:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591691-WellformedReadFilter 2020-05-14T04:31:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591711-SampleReadFilter 2019-12-05T15:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591731-AnalyzeCovariates 2019-12-05T15:10:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591751-RMSMappingQuality 2019-12-05T15:10:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591771-FirstOfPairReadFilter 2019-12-05T15:05:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591791-SecondOfPairReadFilter 2019-12-05T15:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591811-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2019-12-05T15:10:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591831-AnnotatePairOrientation-EXPERIMENTAL 2019-12-05T15:10:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591851-CountReads 2019-12-05T15:10:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591871-FixVcfHeader-Picard 2019-12-05T15:10:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591891-CollectHsMetrics-Picard 2019-12-05T15:10:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591911-GnarlyGenotyper-BETA 2019-12-05T15:10:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591931-EstimateLibraryComplexity-Picard 2019-12-05T15:10:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591951-PrintReadsHeader 2019-12-05T15:10:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591971-ViewSam-Picard 2019-12-05T15:10:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037591991-AnnotateVcfWithExpectedAlleleFraction 2019-12-05T15:10:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592011-CountVariants 2019-12-05T15:10:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592031-AllowAllReadsReadFilter 2019-12-05T15:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592051-NotDuplicateReadFilter 2022-04-01T12:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592071-BamToBfq-Picard 2019-12-05T15:05:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592091-MergePedIntoVcf-Picard 2019-12-05T15:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592111-PrimaryLineReadFilter 2019-12-05T15:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592131-CountBases 2019-12-05T15:10:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592151-StrandOddsRatio 2019-12-05T15:10:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592171-UniqueAltReadCount 2019-12-05T15:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592191-QualByDepth 2019-12-05T15:10:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592211-VariantsToTable 2019-12-05T15:10:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592231-VariantsToTable 2019-12-05T15:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592251-NormalizeFasta-Picard 2019-12-05T15:10:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592271-AS-RMSMappingQuality 2019-12-05T15:10:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592291-CNNVariantWriteTensors-EXPERIMENTAL 2019-12-05T15:10:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592311-CountVariantsSpark 2019-12-05T15:10:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592331-IlluminaBasecallsToFastq-Picard 2019-12-05T15:10:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592351-SamFormatConverter-Picard 2019-12-05T15:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592371-FisherStrand 2019-12-05T15:10:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592391-SoftClippedReadFilter 2024-06-03T12:54:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592411-DepthPerAlleleBySample 2019-12-05T15:10:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592451-SetNmMdAndUqTags-Picard 2019-12-05T15:10:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592471-CompareMetrics-Picard 2019-12-05T15:11:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592491-CompareBaseQualities 2019-12-05T15:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592511-AnnotateVcfWithBamDepth 2019-12-05T15:11:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592531-CollectSequencingArtifactMetrics-Picard 2019-12-05T15:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592551-MappedReadFilter 2019-12-05T15:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592571-ExtractSequences-Picard 2019-12-05T15:11:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592591-GatherBQSRReports 2019-12-05T15:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592611-CpxVariantReInterpreterSpark-BETA 2019-12-05T15:11:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592631-MakeSitesOnlyVcf-Picard 2019-12-05T15:11:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592651-IntervalListTools-Picard 2019-12-05T15:11:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592671-CollectReadCounts 2019-12-05T15:11:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592691-LeftAlignIndels 2019-12-05T15:11:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592711-MappingQualityRankSumTest 2019-12-05T15:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592731-HaplotypeCallerSpark-BETA 2019-12-05T15:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592751-CollectJumpingLibraryMetrics-Picard 2019-12-05T15:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592771-NonNFastaSize-Picard 2019-12-05T15:11:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592811-BaseRecalibratorSpark-BETA 2019-12-05T15:11:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592831-CalculateMixingFractions 2019-12-05T15:11:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592851-GenomicsDBImport 2019-12-05T15:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592871-CreateHadoopBamSplittingIndex-BETA 2019-12-05T15:11:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592891-PrintReads 2019-12-05T15:11:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592911-ValidAlignmentStartReadFilter 2019-12-05T15:11:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592951-ReplaceSamHeader-Picard 2019-12-05T15:11:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592971-MateUnmappedAndUnmappedReadFilter 2019-12-05T15:07:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360037592991-CollectIlluminaLaneMetrics-Picard 2019-12-05T15:11:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593011-CountBasesInReference 2019-12-05T15:11:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593031-PathSeqBwaSpark 2019-12-05T15:11:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593051-SampleList 2019-12-05T15:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593071-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2019-12-05T15:11:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593091-MeanQualityByCycleSpark-BETA 2019-12-05T15:11:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593111-FragmentLength 2019-12-05T15:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593131-CheckIlluminaDirectory-Picard 2019-12-05T15:11:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593151-CollectBaseDistributionByCycle-Picard 2019-12-05T15:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593171-ReblockGVCF-BETA 2019-12-05T15:11:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593191-RevertSamSpark-BETA 2019-12-05T15:11:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593211-ExtractIlluminaBarcodes-Picard 2019-12-05T15:11:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593231-AmbiguousBaseReadFilter 2019-12-05T15:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593251-BedToIntervalList-Picard 2019-12-05T15:11:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593271-CompareDuplicatesSpark-BETA 2019-12-05T15:11:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593291-CollectRawWgsMetrics-Picard 2019-12-05T15:11:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593311-OriginalAlignment 2019-12-05T15:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593331-CreateSequenceDictionary-Picard 2019-12-05T15:11:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593351-VcfToAdpc-Picard 2019-12-05T15:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593371-GoodCigarReadFilter 2024-01-18T00:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593391-PositionBasedDownsampleSam-Picard 2019-12-05T15:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593411-PostprocessGermlineCNVCalls 2022-02-01T15:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593431-PairedReadFilter 2019-12-05T15:08:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593451-GetPileupSummaries 2021-04-17T12:42:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593471-FifoBuffer-Picard 2019-12-05T15:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593511-BaseRecalibrator 2019-12-05T15:12:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593531-RevertBaseQualityScores 2019-12-05T15:12:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593551-GatherTranches-BETA 2019-12-05T15:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593571-CompareSAMs-Picard 2019-12-05T15:12:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593591-BQSRPipelineSpark-BETA 2019-12-05T15:12:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593631-BQSRPipelineSpark-BETA 2019-12-05T15:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593651-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2019-12-05T15:12:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593671-PossibleDeNovo 2023-03-18T05:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593691-DenoiseReadCounts 2019-12-05T15:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593711-BaseQualityRankSumTest 2019-12-05T15:08:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593751-MappingQualityZero 2019-12-05T15:12:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593771-CallCopyRatioSegments 2019-12-05T15:08:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593791-AS-InbreedingCoeff 2019-12-05T15:12:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593811-BamIndexStats-Picard 2019-12-05T15:12:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593831-BamIndexStats-Picard 2019-12-05T15:08:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2 2025-01-04T18:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593871-CollectArraysVariantCallingMetrics-Picard 2019-12-05T15:12:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593891-PlotModeledSegments 2019-12-05T15:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs 2022-08-10T06:41:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593931-CollectGcBiasMetrics-Picard 2019-12-05T15:08:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593951-ReadPosition 2019-12-05T15:08:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593971-Coverage 2020-01-21T13:41:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360037593991-ApplyBQSRSpark-BETA 2019-12-05T15:12:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594011-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2019-12-05T15:08:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594031-CollectMultipleMetrics-Picard 2019-12-05T15:12:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594051-ExtractSVEvidenceSpark-BETA 2019-12-05T15:12:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594071-CollectAllelicCounts 2023-11-17T16:17:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594091-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2019-12-05T15:08:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594111-QualityScoreDistribution-Picard 2019-12-05T15:08:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594131-FlagStat 2019-12-05T15:12:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594151-BaitDesigner-Picard 2019-12-05T15:12:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594171-InbreedingCoeff 2019-12-05T15:08:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594191-ReadLengthEqualsCigarLengthReadFilter 2019-12-05T15:12:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594211-FixMateInformation-Picard 2019-12-05T15:09:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594231-PrintVariantsSpark 2019-12-05T15:12:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594251-ValidateSamFile-Picard 2019-12-05T15:09:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594271-SamToFastq-Picard 2019-12-05T15:12:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594291-SortSam-Picard 2019-12-05T15:12:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594311-FuncotatorDataSourceDownloader 2019-12-05T15:09:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594331-MergeSamFiles-Picard 2019-12-05T15:12:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594351-PathSeqScoreSpark 2019-12-05T15:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594371-FixCallSetSampleOrdering-EXPERIMENTAL 2019-12-05T15:09:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594391-ReadPosRankSumTest 2019-12-05T15:09:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594411-SeqIsStoredReadFilter 2019-12-05T15:09:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594431-IntervalOverlapReadFilter 2019-12-05T15:09:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594451-NonZeroReferenceLengthAlignmentReadFilter 2019-12-05T15:09:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594471-CollectBaseDistributionByCycleSpark-BETA 2019-12-05T15:12:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594511-VariantRecalibrator 2020-09-10T21:15:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594531-PathSeqFilterSpark 2019-12-05T15:12:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594551-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2019-12-05T15:12:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker 2020-12-08T07:00:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594591-EvaluateInfoFieldConcordance-BETA 2019-12-05T15:12:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594611-SplitNCigarReads 2019-12-05T15:12:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594631-NonZeroFragmentLengthReadFilter 2019-12-05T15:09:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594651-PileupSpark-BETA 2019-12-05T15:12:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594671-SplitVcfs-Picard 2019-12-05T15:13:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594711-CrosscheckFingerprints-Picard 2023-02-23T22:38:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594731-GenotypeGVCFs 2019-12-05T15:13:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594751-FindBadGenomicKmersSpark-BETA 2019-12-05T15:13:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594771-AnalyzeSaturationMutagenesis-BETA 2019-12-05T15:13:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594791-AS-BaseQualityRankSumTest 2019-12-05T15:13:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594811-CollectRrbsMetrics-Picard 2019-12-05T15:09:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594831-FindMendelianViolations-Picard 2019-12-05T15:13:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594851-IndexFeatureFile 2019-12-05T15:09:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594871-MetricsReadFilter 2019-12-05T15:09:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594891-AlleleFraction 2023-05-21T23:12:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594911-ConvertSequencingArtifactToOxoG-Picard 2019-12-05T15:09:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594931-CountNs 2019-12-05T15:09:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594951-RenameSampleInVcf-Picard 2019-12-05T15:13:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594971-MappingQualityAvailableReadFilter 2019-12-05T15:09:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360037594991-CountReadsSpark 2019-12-05T15:13:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037595011-CountBasesSpark 2019-12-05T15:13:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360037595031-GtcToVcf-Picard 2019-12-05T15:10:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360037595051-CheckTerminatorBlock-Picard 2019-12-05T15:10:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360037595071-CleanSam-Picard 2019-12-05T15:10:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360037872491--How-to-Fix-a-badly-formatted-BAM 2024-06-25T07:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360038096372-Catching-up-with-the-times-GATK-is-moving-to-a-new-web-home 2020-01-04T15:43:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360038154292-Welcome-to-the-new-home-of-GATK 2021-09-01T14:46:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360039532132--GATK-Workshop-in-San-Jos%C3%A9-Costa-Rica-Feb-11-14-2020 2024-07-08T20:10:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360039568932--How-to-Map-and-clean-up-short-read-sequence-data-efficiently 2024-06-25T07:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360039984151-DRAGEN-GATK-Update-Let-s-get-more-specific 2023-10-14T18:04:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095592-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2020-03-04T19:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095612-ChromosomeCounts 2020-03-04T19:51:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095632-CollectHiSeqXPfFailMetrics-Picard 2020-03-04T19:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095652-BwaMemIndexImageCreator 2022-04-15T01:40:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095672-WellformedReadFilter 2020-03-04T19:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095692-FirstOfPairReadFilter 2020-03-04T19:51:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095712-CalcMetadataSpark-BETA 2020-03-04T19:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095732-AlignmentAgreesWithHeaderReadFilter 2020-03-04T19:51:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095752-AnnotatePairOrientation-EXPERIMENTAL 2020-03-04T19:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095772-PrintReadsHeader 2020-03-04T19:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095792-AnnotateVcfWithExpectedAlleleFraction 2020-03-04T19:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095812-LiftOverIntervalList-Picard 2020-03-04T19:51:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095832-NotDuplicateReadFilter 2020-03-04T19:51:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095852-BamToBfq-Picard 2020-03-04T19:51:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095872-VariantAnnotator 2020-03-04T19:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095892-PrimaryLineReadFilter 2020-03-04T19:51:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095912-CountBases 2020-03-04T19:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095932-StrandOddsRatio 2020-03-04T19:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095952-CheckFingerprint-Picard 2020-03-04T19:51:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095972-HasReadGroupReadFilter 2020-03-04T19:51:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360040095992-FindBreakpointEvidenceSpark-BETA 2020-03-04T19:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096032-QualByDepth 2020-03-04T19:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096052-VariantsToTable 2020-03-04T19:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096072-NormalizeFasta-Picard 2020-03-04T19:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096092-AS-RMSMappingQuality 2020-03-04T19:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096112-CNNVariantWriteTensors-EXPERIMENTAL 2020-03-04T19:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096132-SamFormatConverter-Picard 2020-03-04T19:52:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096152-FisherStrand 2020-03-04T19:55:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096172-CollectSamErrorMetrics-Picard 2020-03-04T19:52:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096192-GetSampleName 2020-03-04T19:55:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096212-MarkDuplicatesSpark 2020-03-04T19:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096232-CalculateReadGroupChecksum-Picard 2020-03-04T19:56:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096252-SetNmMdAndUqTags-Picard 2020-03-04T19:56:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096272-GatherBamFiles-Picard 2020-03-04T19:52:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096292-CalculateFingerprintMetrics-Picard 2020-03-04T19:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096312-PathSeqBuildReferenceTaxonomy 2020-03-04T19:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096332-BwaSpark-BETA 2020-03-04T19:56:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096352-MappedReadFilter 2020-03-04T19:52:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096372-ExtractSequences-Picard 2020-03-04T19:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096392-AlleleFrequency 2020-03-04T19:52:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096432-GatherBQSRReports 2020-03-04T19:52:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096452-CpxVariantReInterpreterSpark-BETA 2020-03-04T19:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096472-IntervalListTools-Picard 2020-03-04T19:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096492-StrandBiasBySample 2020-03-04T19:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096512-SortSamSpark-BETA 2020-03-04T19:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096532-MappingQualityRankSumTest 2020-03-04T19:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096552-MappingQualityNotZeroReadFilter 2020-03-04T19:52:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096572-CollectJumpingLibraryMetrics-Picard 2020-03-04T19:52:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096592-MateDifferentStrandReadFilter 2020-03-04T19:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096612-NonNFastaSize-Picard 2020-03-04T19:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096652-FilterMutectCalls 2020-03-04T19:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096672-BaseRecalibratorSpark-BETA 2020-03-04T19:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096692-AccumulateVariantCallingMetrics-Picard 2020-03-04T19:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096712-MappingQualityReadFilter 2020-03-04T19:56:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096732-GenomicsDBImport 2020-06-25T04:12:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096752-CollectQualityYieldMetricsSpark-BETA 2020-03-04T19:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096772-PlatformUnitReadFilter 2020-03-04T19:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096792-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-03-04T19:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096812-HaplotypeCaller 2020-03-04T19:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096832-ValidAlignmentStartReadFilter 2020-03-04T19:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096852-MateUnmappedAndUnmappedReadFilter 2020-03-04T19:52:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096872-CollectIlluminaLaneMetrics-Picard 2020-03-04T19:56:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096892-CountBasesInReference 2020-03-04T19:56:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096912-VcfToIntervalList-Picard 2020-03-04T19:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096932-MarkIlluminaAdapters-Picard 2020-03-04T19:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096952-SampleList 2020-03-04T19:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096972-MeanQualityByCycleSpark-BETA 2020-03-04T19:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040096992-FragmentLength 2020-03-04T19:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097012-CollectTargetedPcrMetrics-Picard 2020-03-04T19:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097032-CollectBaseDistributionByCycle-Picard 2020-03-04T19:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097052-ReblockGVCF-BETA 2020-03-04T19:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097072-MergeBamAlignment-Picard 2020-03-04T19:53:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097092-FixMisencodedBaseQualityReads 2020-03-04T19:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097112-LeftAlignAndTrimVariants 2020-03-04T19:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097132-RevertSamSpark-BETA 2020-03-04T19:56:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097152-ExtractIlluminaBarcodes-Picard 2020-03-04T19:56:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097172-BedToIntervalList-Picard 2020-03-04T19:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097192-RemoveNearbyIndels 2020-03-04T19:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097212-FilterByOrientationBias-EXPERIMENTAL 2020-03-04T19:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097252-MarkDuplicates-Picard 2020-03-04T19:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097272-CreateSequenceDictionary-Picard 2020-03-04T19:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097292-VcfToAdpc-Picard 2020-03-04T19:53:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097312-GoodCigarReadFilter 2020-03-04T19:53:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097332-PositionBasedDownsampleSam-Picard 2020-03-04T19:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097352-PostprocessGermlineCNVCalls 2020-03-04T19:56:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097372-CollectWgsMetrics-Picard 2020-03-04T19:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097392-PairedReadFilter 2020-03-04T19:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097412-AS-ReadPosRankSumTest 2020-03-04T19:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097432-GetPileupSummaries 2020-03-04T19:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097452-FifoBuffer-Picard 2020-03-04T19:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097492-ExcessHet 2020-03-04T19:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097512-LikelihoodRankSumTest 2020-03-04T19:53:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097532-BaseRecalibrator 2020-03-05T16:12:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097552-RevertBaseQualityScores 2020-03-04T19:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097572-DownsampleSam-Picard 2020-03-04T19:56:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097592-CompareSAMs-Picard 2020-03-04T19:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097612-BQSRPipelineSpark-BETA 2020-03-04T19:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097632-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-03-04T19:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097652-BaseQualityRankSumTest 2020-03-04T19:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097712-GermlineCNVCaller 2020-03-04T19:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097732-UpdateVcfSequenceDictionary-Picard 2020-03-04T19:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097752-ReadNameReadFilter 2020-03-04T19:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097772-MappingQualityZero 2020-03-04T19:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097792-CallCopyRatioSegments 2020-03-04T19:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097812-PlatformReadFilter 2020-03-04T19:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097832-BamIndexStats-Picard 2020-03-04T19:57:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097852-Mutect2 2020-03-30T03:22:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097872-CollectArraysVariantCallingMetrics-Picard 2020-03-04T19:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097912-PlotModeledSegments 2020-03-04T19:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097932-CollectGcBiasMetrics-Picard 2020-03-04T19:53:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097952-ReadStrandFilter 2020-03-04T19:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097972-ApplyBQSRSpark-BETA 2020-03-04T19:57:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360040097992-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-03-04T19:54:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098012-CalculateGenotypePosteriors 2020-03-04T19:57:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098032-MergeVcfs-Picard 2020-03-04T19:57:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098052-CollectMultipleMetrics-Picard 2020-03-04T19:57:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098072-PreprocessIntervals 2020-03-04T19:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098092-QualityScoreDistribution-Picard 2020-03-04T19:54:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098112-FlagStat 2020-03-04T19:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098132-FixMateInformation-Picard 2020-03-04T19:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098152-PrintVariantsSpark 2020-03-04T19:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098172-ValidateSamFile-Picard 2020-03-04T19:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098192-SortSam-Picard 2020-03-04T19:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098212-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-03-04T19:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098232-GatherVcfsCloud-BETA 2020-03-04T19:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098252-AnnotateIntervals 2020-03-04T19:57:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098272-PathSeqScoreSpark 2020-03-04T19:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098292-PassesVendorQualityCheckReadFilter 2020-03-04T19:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098312-ReadPosRankSumTest 2020-03-04T19:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098332-BaseQuality 2021-04-13T08:12:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098352-SeqIsStoredReadFilter 2020-03-04T19:54:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098372-NonZeroReferenceLengthAlignmentReadFilter 2020-03-04T19:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098412-PathSeqFilterSpark 2020-03-04T19:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098432-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-03-04T19:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098452-StructuralVariationDiscoveryPipelineSpark-BETA 2020-03-04T19:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098472-EvaluateInfoFieldConcordance-BETA 2020-03-04T19:57:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098492-SplitNCigarReads 2020-03-04T19:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098512-CigarContainsNoNOperator 2020-03-04T19:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098532-SplitVcfs-Picard 2020-03-04T19:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098552-FilterFuncotations-EXPERIMENTAL 2020-03-04T19:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098572-SplitSamByLibrary-Picard 2020-03-04T19:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098592-CrosscheckFingerprints-Picard 2020-03-04T19:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098612-FindBadGenomicKmersSpark-BETA 2020-03-04T19:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098632-AddCommentsToBam-Picard 2020-03-04T19:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098652-AnalyzeSaturationMutagenesis-BETA 2020-03-04T19:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098672-AS-BaseQualityRankSumTest 2020-03-04T19:57:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098692-FragmentLengthReadFilter 2020-03-04T19:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098712-BuildBamIndex-Picard 2020-03-04T19:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098732-CollectRrbsMetrics-Picard 2020-03-04T19:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098752-NotSecondaryAlignmentReadFilter 2020-03-04T19:55:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098772-FindMendelianViolations-Picard 2020-03-04T19:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098792-ReferenceBases 2020-03-04T19:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098812-OrientationBiasReadCounts 2020-03-04T19:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098832-MappingQualityAvailableReadFilter 2020-03-04T19:55:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098852-CollectOxoGMetrics-Picard 2020-03-04T19:55:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098872-CountBasesSpark 2020-03-04T19:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098892-PrintReadsSpark 2020-03-04T19:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360040098912-FilterVariantTranches 2020-03-04T19:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506771-LibraryReadFilter 2020-03-04T19:51:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506791-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2020-03-04T19:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506811-NonChimericOriginalAlignmentReadFilter 2020-03-04T19:51:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506831-MeanQualityByCycle-Picard 2020-03-04T19:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506871-GenotypeConcordance-Picard 2020-03-04T19:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506891-Pileup 2020-03-04T19:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506911-OverclippedReadFilter 2020-03-04T19:51:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506931-NotProperlyPairedReadFilter 2020-03-04T19:51:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506951-SampleReadFilter 2020-03-04T19:51:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506971-AnalyzeCovariates 2020-03-04T19:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360040506991-RMSMappingQuality 2020-03-04T19:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507011-Funcotator 2020-03-04T19:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507031-CollectQualityYieldMetrics-Picard 2020-03-04T19:51:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507071-PathSeqPipelineSpark 2020-03-04T19:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507091-SecondOfPairReadFilter 2020-03-04T19:51:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507111-AS-StrandOddsRatio 2020-03-04T19:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507131-FilterVcf-Picard 2020-03-04T19:51:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507151-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-03-04T19:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507171-VariantEval-BETA 2020-03-04T19:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507191-CountReads 2020-03-04T19:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507211-FixVcfHeader-Picard 2020-03-04T19:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507231-CollectHsMetrics-Picard 2020-03-04T19:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507251-GnarlyGenotyper-BETA 2020-03-04T19:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507271-EstimateLibraryComplexity-Picard 2020-03-04T19:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507291-ViewSam-Picard 2020-03-04T19:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507311-CountVariants 2020-03-04T19:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507331-AllowAllReadsReadFilter 2020-03-04T19:51:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507351-FilterSamReads-Picard 2020-03-04T19:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507371-MergePedIntoVcf-Picard 2020-03-04T19:51:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507411-CollectMultipleMetricsSpark-BETA 2020-03-04T19:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507431--Tool-Documentation-Index 2020-03-06T17:20:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507451-DetermineGermlineContigPloidy 2020-03-04T19:51:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507471-UniqueAltReadCount 2020-03-04T19:51:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507491-MappingQuality 2020-03-04T19:51:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507511-CountVariantsSpark 2020-03-04T19:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507531-UpdateVCFSequenceDictionary 2020-03-04T19:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507551-IlluminaBasecallsToFastq-Picard 2020-03-04T19:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507571-ClusterCrosscheckMetrics-Picard 2020-03-04T19:52:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507591-ClipReads 2020-03-04T19:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507611-SoftClippedReadFilter 2020-03-04T19:52:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507631-DepthPerAlleleBySample 2020-03-04T19:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507651-CompareMetrics-Picard 2020-03-04T19:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507671-FuncotateSegments-BETA 2020-03-04T19:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507711-AS-FisherStrand 2020-03-04T19:56:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507731-CompareBaseQualities 2020-03-04T19:52:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507751-CollectAlignmentSummaryMetrics-Picard 2020-03-04T19:52:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507771-AnnotateVcfWithBamDepth 2020-03-04T19:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507791-CollectSequencingArtifactMetrics-Picard 2020-03-04T19:52:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507811-GatherVcfs-Picard 2020-03-04T19:52:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507831-MarkDuplicatesWithMateCigar-Picard 2020-03-04T19:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507851-CalculateContamination 2020-03-04T19:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507871-ApplyBQSR 2020-03-04T19:56:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507891-PathSeqBuildKmers 2020-03-04T19:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507911-MakeSitesOnlyVcf-Picard 2020-03-04T19:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507931-CollectInsertSizeMetrics-Picard 2023-04-23T01:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507951-CollectReadCounts 2020-03-04T19:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507971-LeftAlignIndels 2020-03-04T19:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360040507991-FilterIntervals 2020-03-04T19:52:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508011-HaplotypeCallerSpark-BETA 2020-03-04T19:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508031-SplitSamByNumberOfReads-Picard 2020-03-04T19:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508051-CalculateMixingFractions 2020-03-04T19:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508071-SelectVariants 2020-03-04T19:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508091-IlluminaBasecallsToSam-Picard 2020-03-04T19:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508111-ReadGroupReadFilter 2020-03-04T19:52:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508131-CreateHadoopBamSplittingIndex-BETA 2020-03-04T19:56:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508151-PrintReads 2020-03-04T19:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508171-MateDistantReadFilter 2020-03-04T19:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508191-ReadsPipelineSpark-BETA 2020-03-04T19:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508211-ReplaceSamHeader-Picard 2020-03-04T19:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508231-CountFalsePositives-BETA 2020-03-04T19:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508251-SetNmAndUqTags-Picard 2020-03-04T19:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508271-PathSeqBwaSpark 2020-03-04T19:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508291-MatchingBasesAndQualsReadFilter 2020-03-04T19:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508311-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-03-04T19:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508331-CheckIlluminaDirectory-Picard 2020-03-04T19:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508351-ModelSegments 2020-03-04T19:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508371-AmbiguousBaseReadFilter 2020-03-04T19:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508391-CompareDuplicatesSpark-BETA 2020-03-04T19:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508411-CollectRawWgsMetrics-Picard 2020-03-04T19:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508431-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-03-04T19:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508451-OriginalAlignment 2020-03-04T19:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508471-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-03-04T19:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508491-ReorderSam-Picard 2020-03-04T19:53:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508511-NotSupplementaryAlignmentReadFilter 2020-03-04T19:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508531-GenotypeSummaries 2020-03-04T19:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508551-FlagStatSpark 2020-03-04T19:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508571-FilterAlignmentArtifacts-EXPERIMENTAL 2020-03-04T19:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508611-VariantFiltration 2020-03-04T19:56:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508631-GatherTranches-BETA 2020-03-04T19:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508671-ClippingRankSumTest 2020-03-04T19:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508691-PossibleDeNovo 2020-03-04T19:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508711-CollectInsertSizeMetricsSpark-BETA 2020-03-04T19:57:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508731-DenoiseReadCounts 2020-03-04T19:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508751-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-03-04T19:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508771-IntervalListToBed-Picard 2020-03-04T19:53:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508791-ApplyVQSR 2020-03-04T19:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508811-ScatterIntervalsByNs-Picard 2020-03-04T19:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508831-AS-InbreedingCoeff 2020-03-04T19:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508871-VcfFormatConverter-Picard 2020-03-04T19:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508891-AddOrReplaceReadGroups-Picard 2020-03-04T19:53:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508931-CollectVariantCallingMetrics-Picard 2020-03-04T19:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508971-CombineGVCFs 2020-03-04T19:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360040508991-LiftoverVcf-Picard 2020-03-04T19:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509011-AddOATag-Picard 2020-03-04T19:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509031-ReadPosition 2020-03-04T19:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509051-MateOnSameContigOrNoMappedMateReadFilter 2020-03-04T19:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509071-Coverage 2020-03-04T19:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509091-ValidateVariants 2020-03-04T19:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509111-ExtractSVEvidenceSpark-BETA 2020-03-04T19:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509131-CollectAllelicCounts 2020-03-04T19:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509151-CNNScoreVariants 2020-03-04T19:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509171-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-03-04T19:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509191-MethylationTypeCaller-EXPERIMENTAL 2020-03-04T19:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509211-CombineGenotypingArrayVcfs-Picard 2020-03-04T19:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509231-BaitDesigner-Picard 2020-03-04T19:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509251-InbreedingCoeff 2020-03-04T19:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509271-ReadLengthEqualsCigarLengthReadFilter 2020-03-04T19:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509291-SortVcf-Picard 2020-03-04T19:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509311-FastqToSam-Picard 2020-03-04T19:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509331-ReadGroupBlackListReadFilter 2020-03-04T19:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509351-SamToFastq-Picard 2020-03-04T19:57:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509371-CollectIlluminaBasecallingMetrics-Picard 2020-03-04T19:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509391-FuncotatorDataSourceDownloader 2024-12-16T16:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509411-MergeSamFiles-Picard 2020-03-04T19:57:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509431-CollectRnaSeqMetrics-Picard 2020-03-04T19:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509451-RevertSam-Picard 2020-03-04T19:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509471-SplitReads 2020-03-04T19:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509491-AS-MappingQualityRankSumTest 2020-03-04T19:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509511-FixCallSetSampleOrdering-EXPERIMENTAL 2020-03-04T19:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509531-IntervalOverlapReadFilter 2020-03-04T19:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509551-CollectBaseDistributionByCycleSpark-BETA 2020-03-04T19:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509571-VariantRecalibrator 2020-03-04T19:57:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509591-PlotDenoisedCopyRatios 2021-04-28T04:10:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509611-SplitIntervals 2020-03-04T19:57:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509631-FastaAlternateReferenceMaker 2020-03-04T19:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509651-UnmarkDuplicates 2020-03-04T19:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509671-NonZeroFragmentLengthReadFilter 2020-03-04T19:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509691-PileupSpark-BETA 2020-03-04T19:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509711-ProperlyPairedReadFilter 2020-03-04T19:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509731-CNNVariantTrain-EXPERIMENTAL 2020-03-04T19:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509751-GenotypeGVCFs 2020-03-04T19:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509771-TandemRepeat 2020-03-04T19:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509791-AS-QualByDepth 2020-03-04T19:57:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509811-Concordance 2020-03-04T19:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509831-IndexFeatureFile 2020-03-04T19:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509851-MetricsReadFilter 2020-03-04T19:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509871-ValidAlignmentEndReadFilter 2020-03-04T19:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509891-FastaReferenceMaker 2020-03-04T19:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509911-QualityScoreDistributionSpark-BETA 2020-03-04T19:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509931-DepthPerSampleHC 2020-03-04T19:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509951-AlleleFraction 2020-03-04T19:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509971-ConvertSequencingArtifactToOxoG-Picard 2020-03-04T19:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360040509991-CountNs 2020-03-04T19:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510011-RenameSampleInVcf-Picard 2020-03-04T19:58:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510031-CreateReadCountPanelOfNormals 2020-03-04T19:55:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510051-CollectDuplicateMetrics-Picard 2020-03-04T19:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510071-CountReadsSpark 2020-03-04T19:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510111-ASEReadCounter 2020-03-04T19:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510131-CreateSomaticPanelOfNormals-BETA 2020-03-04T19:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510151-CheckPileup 2020-03-04T19:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510171-GtcToVcf-Picard 2020-03-04T19:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510191-CheckTerminatorBlock-Picard 2020-03-04T19:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510211-ReadLengthReadFilter 2020-03-04T19:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360040510231-CleanSam-Picard 2020-03-04T19:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360040762872-GATK-Workshops-Cancellations-Rescheduling 2024-07-01T17:20:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360040843831--GATK-Workshop-in-Gujarat-India-Mar-2-5-2020 2024-07-08T20:10:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360041155232-Reference-Genome-Components 2024-06-25T07:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices 2024-06-25T07:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360041413932-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2020-04-02T19:00:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360041413952-ChromosomeCounts 2020-04-02T18:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360041413972-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2020-04-02T19:00:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360041413992-NonChimericOriginalAlignmentReadFilter 2020-04-02T18:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414012-CollectHiSeqXPfFailMetrics-Picard 2020-04-02T19:00:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414032-OverclippedReadFilter 2020-04-02T18:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414072-NotProperlyPairedReadFilter 2020-04-02T18:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414092-WellformedReadFilter 2020-04-02T19:01:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414112-AnalyzeCovariates 2020-04-02T19:01:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414132-CollectQualityYieldMetrics-Picard 2020-04-02T18:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414152-PathSeqPipelineSpark 2020-04-02T19:01:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414172-CalcMetadataSpark-BETA 2020-04-02T19:01:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414192-AlignmentAgreesWithHeaderReadFilter 2020-04-02T18:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414212-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-04-02T19:01:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414232-AnnotatePairOrientation-EXPERIMENTAL 2020-04-02T19:01:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414252-VariantEval-BETA 2020-04-02T19:01:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414272-CountReads 2020-04-02T19:01:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414312-EstimateLibraryComplexity-Picard 2020-04-02T19:01:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414332-PrintReadsHeader 2020-04-02T19:01:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414352-LiftOverIntervalList-Picard 2020-04-02T18:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414372-VariantAnnotator 2023-03-07T19:45:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414392-FilterSamReads-Picard 2020-04-02T19:01:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414412-PrimaryLineReadFilter 2020-04-02T18:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414432-CountBases 2020-04-02T19:01:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414452--Tool-Documentation-Index 2020-04-02T19:46:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414472-CheckFingerprint-Picard 2020-04-02T18:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414492-HasReadGroupReadFilter 2020-04-02T18:56:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414512-DetermineGermlineContigPloidy 2020-04-02T18:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414532-FindBreakpointEvidenceSpark-BETA 2020-04-02T19:01:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414552-MappingQuality 2020-04-02T18:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414572-QualByDepth 2020-04-02T19:01:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414592-VariantsToTable 2020-04-02T19:01:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414612-AS-RMSMappingQuality 2020-04-02T19:01:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414632-CNNVariantWriteTensors-EXPERIMENTAL 2020-04-02T19:01:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414672-SamFormatConverter-Picard 2020-04-02T18:57:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414692-FisherStrand 2020-04-02T19:01:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414712-SoftClippedReadFilter 2020-04-02T18:57:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414752-DepthPerAlleleBySample 2020-04-02T19:01:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414772-CalculateReadGroupChecksum-Picard 2020-04-02T19:01:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414792-FuncotateSegments-BETA 2020-04-02T19:01:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414812-GatherBamFiles-Picard 2020-04-02T18:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414832-PathSeqBuildReferenceTaxonomy 2020-04-02T18:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414872-CompareBaseQualities 2020-04-02T18:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414912-CollectAlignmentSummaryMetrics-Picard 2020-04-02T18:57:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414932-AnnotateVcfWithBamDepth 2020-04-02T19:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414952-GatherBQSRReports 2020-04-02T18:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414972-CalculateContamination 2020-04-02T19:01:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360041414992-CollectInsertSizeMetrics-Picard 2020-04-02T18:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415012-SortSamSpark-BETA 2020-04-02T19:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415032-LeftAlignIndels 2020-04-02T19:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415052-MappingQualityRankSumTest 2020-04-02T19:02:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415072-CollectJumpingLibraryMetrics-Picard 2020-04-02T18:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415092-NonNFastaSize-Picard 2020-04-02T19:02:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415112-BaseRecalibratorSpark-BETA 2020-04-02T19:02:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415132-CalculateMixingFractions 2020-04-02T19:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415152-IlluminaBasecallsToSam-Picard 2020-04-02T19:02:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415172-ReadGroupReadFilter 2020-04-02T18:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415192-MappingQualityReadFilter 2020-04-02T19:02:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415212-GenomicsDBImport 2020-05-09T07:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415252-PlatformUnitReadFilter 2020-04-02T18:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415272-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-04-02T19:02:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415292-HaplotypeCaller 2020-04-02T19:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415332-ReplaceSamHeader-Picard 2020-04-02T19:02:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415352-MateUnmappedAndUnmappedReadFilter 2020-04-02T18:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415372-CountBasesInReference 2020-04-02T19:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415412-VcfToIntervalList-Picard 2020-04-02T19:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415432-SetNmAndUqTags-Picard 2020-04-02T19:02:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415452-PathSeqBwaSpark 2020-04-02T19:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415472-MarkIlluminaAdapters-Picard 2020-04-02T19:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415492-MatchingBasesAndQualsReadFilter 2020-04-02T18:58:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415512-MeanQualityByCycleSpark-BETA 2020-04-02T19:02:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415532-FragmentLength 2020-04-02T18:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415552-CollectTargetedPcrMetrics-Picard 2020-04-02T19:02:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415572-ReblockGVCF-BETA 2020-04-02T19:02:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415612-ExtractIlluminaBarcodes-Picard 2020-04-02T19:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415632-AmbiguousBaseReadFilter 2020-04-02T18:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415652-BedToIntervalList-Picard 2020-04-02T19:02:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415672-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-04-02T19:02:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415692-OriginalAlignment 2020-04-02T18:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415712-MarkDuplicates-Picard 2020-04-02T19:02:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415732-CreateSequenceDictionary-Picard 2020-04-02T19:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415752-VcfToAdpc-Picard 2020-04-02T18:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415772-GoodCigarReadFilter 2020-04-02T18:58:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415792-ReorderSam-Picard 2020-04-02T18:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415812-PostprocessGermlineCNVCalls 2020-04-02T19:02:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415832-FilterAlignmentArtifacts-EXPERIMENTAL 2020-04-02T19:02:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415852-CollectWgsMetrics-Picard 2020-04-02T19:02:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415872-AS-ReadPosRankSumTest 2020-04-02T19:02:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415912-GatherTranches-BETA 2020-04-02T18:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415932-ClippingRankSumTest 2020-04-02T18:58:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415972-CompareSAMs-Picard 2020-04-02T19:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360041415992-BQSRPipelineSpark-BETA 2020-04-02T19:02:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416012-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-04-02T19:02:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416032-DenoiseReadCounts 2020-04-02T18:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416072-ScatterIntervalsByNs-Picard 2020-04-02T19:03:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416092-AS-InbreedingCoeff 2020-04-02T19:03:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416112-Mutect2 2020-04-02T19:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416132-CollectArraysVariantCallingMetrics-Picard 2020-04-02T19:03:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416152-VcfFormatConverter-Picard 2020-04-02T19:03:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416172-PlotModeledSegments 2021-04-14T09:02:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416192-CollectVariantCallingMetrics-Picard 2020-04-02T18:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416212-CombineGVCFs 2021-09-18T01:16:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416232-MateOnSameContigOrNoMappedMateReadFilter 2020-04-02T19:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416252-ReadStrandFilter 2020-04-02T18:59:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416272-ApplyBQSRSpark-BETA 2020-04-02T19:03:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416292-CalculateGenotypePosteriors 2020-04-02T19:03:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416312-MergeVcfs-Picard 2020-04-02T19:03:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416332-ValidateVariants 2020-04-02T19:03:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416352-ExtractSVEvidenceSpark-BETA 2020-04-02T19:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416372-CollectAllelicCounts 2020-04-02T19:03:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416392-CNNScoreVariants 2020-04-02T19:03:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416412-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-04-02T18:59:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416432-MethylationTypeCaller-EXPERIMENTAL 2020-04-02T19:03:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416452-PreprocessIntervals 2020-04-02T19:03:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416472-QualityScoreDistribution-Picard 2020-04-02T18:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416492-BaitDesigner-Picard 2020-04-02T19:03:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416512-ReadLengthEqualsCigarLengthReadFilter 2020-04-02T19:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416532-SortVcf-Picard 2020-04-02T19:03:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416552-FastqToSam-Picard 2020-04-02T19:03:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416572-SamToFastq-Picard 2020-04-02T19:03:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416592-SortSam-Picard 2020-04-02T19:03:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416612-MergeSamFiles-Picard 2020-04-02T19:03:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416632-GatherVcfsCloud-BETA 2020-04-02T19:03:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416652-AnnotateIntervals 2020-04-02T19:03:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416672-PassesVendorQualityCheckReadFilter 2020-04-02T18:59:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416692-SplitReads 2020-04-02T19:03:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416712-AS-MappingQualityRankSumTest 2020-04-02T19:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416752-FixCallSetSampleOrdering-EXPERIMENTAL 2020-04-02T19:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416792-IntervalOverlapReadFilter 2020-04-02T19:00:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416812-CollectBaseDistributionByCycleSpark-BETA 2020-04-02T19:03:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416832-PathSeqFilterSpark 2020-04-02T19:03:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416852-PlotDenoisedCopyRatios 2020-04-02T19:00:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416872-FastaAlternateReferenceMaker 2020-04-02T19:03:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416892-StructuralVariationDiscoveryPipelineSpark-BETA 2020-04-02T19:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416912-EvaluateInfoFieldConcordance-BETA 2020-04-02T19:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416932-SplitNCigarReads 2020-04-02T19:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416952-NonZeroFragmentLengthReadFilter 2020-04-02T19:00:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416972-PileupSpark-BETA 2020-04-02T19:03:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360041416992-CigarContainsNoNOperator 2020-04-02T19:00:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417012-SplitVcfs-Picard 2020-04-02T19:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417032-SplitSamByLibrary-Picard 2020-04-02T19:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417052-CrosscheckFingerprints-Picard 2020-04-02T19:03:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417072-CNNVariantTrain-EXPERIMENTAL 2020-04-02T19:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417092-GenotypeGVCFs 2020-04-02T19:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417112-FindBadGenomicKmersSpark-BETA 2020-04-02T19:04:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417132-AddCommentsToBam-Picard 2020-04-02T19:04:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417152-AS-BaseQualityRankSumTest 2020-04-02T19:04:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417172-NotSecondaryAlignmentReadFilter 2020-04-02T19:00:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417212-ReferenceBases 2020-04-02T19:00:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417292-ConvertSequencingArtifactToOxoG-Picard 2020-04-02T19:00:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417312-CountNs 2020-04-02T19:00:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417332-RenameSampleInVcf-Picard 2020-04-02T19:04:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417352-CollectOxoGMetrics-Picard 2020-04-02T19:00:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417372-CountReadsSpark 2020-04-02T19:04:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417392-PrintReadsSpark 2020-04-02T19:04:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417412-FilterVariantTranches 2020-04-02T19:04:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417432-CreateSomaticPanelOfNormals-BETA 2020-04-02T19:04:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360041417452-CheckPileup 2020-04-02T19:04:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360041583191-Hosting-Requirements-for-a-Workshop 2024-07-08T20:11:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360041583371-Missing-physical-phasing-information-in-vcf 2024-06-25T07:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360041696232-Detecting-sample-swaps-with-Picard-tools 2023-10-05T10:19:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848651-LibraryReadFilter 2020-04-02T18:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848671-MeanQualityByCycle-Picard 2020-04-02T19:00:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848691-GenotypeConcordance-Picard 2020-04-02T19:00:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848711-Pileup 2020-04-02T19:01:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848731-BwaMemIndexImageCreator 2020-04-02T19:01:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848751-SampleReadFilter 2020-04-02T18:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848771-RMSMappingQuality 2020-04-02T19:01:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848791-FirstOfPairReadFilter 2020-04-02T18:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848811-Funcotator 2020-04-11T20:43:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848831-SecondOfPairReadFilter 2020-04-02T18:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848851-AS-StrandOddsRatio 2020-04-02T19:01:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848871-FilterVcf-Picard 2020-04-02T18:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848891-FixVcfHeader-Picard 2020-04-02T19:01:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848911-CollectHsMetrics-Picard 2020-04-02T19:01:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848931-GnarlyGenotyper-BETA 2020-04-02T19:01:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848951-ViewSam-Picard 2020-04-02T19:01:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848971-AnnotateVcfWithExpectedAlleleFraction 2020-04-02T19:01:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360041848991-CountVariants 2020-04-02T19:01:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849011-AllowAllReadsReadFilter 2020-04-02T18:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849031-NotDuplicateReadFilter 2020-04-02T18:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849051-BamToBfq-Picard 2020-04-02T18:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849071-MergePedIntoVcf-Picard 2020-04-02T18:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849091-CollectMultipleMetricsSpark-BETA 2020-04-02T19:01:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849111-StrandOddsRatio 2020-04-02T19:01:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849131-UniqueAltReadCount 2020-04-02T18:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849151-NormalizeFasta-Picard 2020-04-02T19:01:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849171-CountVariantsSpark 2020-04-02T19:01:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849191-UpdateVCFSequenceDictionary 2020-04-02T19:01:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849211-IlluminaBasecallsToFastq-Picard 2020-04-02T19:01:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849231-ClusterCrosscheckMetrics-Picard 2020-04-02T18:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849251-ClipReads 2020-04-02T19:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849271-CollectSamErrorMetrics-Picard 2020-04-02T18:57:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849311-GetSampleName 2020-04-02T19:01:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849331-MarkDuplicatesSpark 2020-04-02T19:01:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849351-SetNmMdAndUqTags-Picard 2020-04-02T19:01:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849371-CompareMetrics-Picard 2020-04-02T19:01:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849391-CalculateFingerprintMetrics-Picard 2020-04-02T18:57:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849411-AS-FisherStrand 2020-04-02T19:01:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849431-BwaSpark-BETA 2020-04-02T19:01:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849451-CollectSequencingArtifactMetrics-Picard 2020-04-02T18:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849471-GatherVcfs-Picard 2020-04-02T18:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849491-MappedReadFilter 2020-04-02T18:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849511-ExtractSequences-Picard 2020-04-02T19:01:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849531-MarkDuplicatesWithMateCigar-Picard 2020-04-02T19:01:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849551-AlleleFrequency 2020-04-02T18:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849571-ApplyBQSR 2023-12-03T05:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849591-CpxVariantReInterpreterSpark-BETA 2020-04-02T19:01:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849611-PathSeqBuildKmers 2020-04-02T19:01:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849631-MakeSitesOnlyVcf-Picard 2020-04-02T19:01:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849651-IntervalListTools-Picard 2020-04-02T19:01:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849671-StrandBiasBySample 2020-04-02T19:01:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849691-CollectReadCounts 2020-04-02T19:01:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849711-FilterIntervals 2020-04-02T18:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849731-MappingQualityNotZeroReadFilter 2020-04-02T18:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849751-HaplotypeCallerSpark-BETA 2020-04-02T19:02:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849771-SplitSamByNumberOfReads-Picard 2020-04-02T19:02:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849791-MateDifferentStrandReadFilter 2020-04-02T19:02:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849811-FilterMutectCalls 2020-04-02T19:02:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849831-SelectVariants 2020-04-02T19:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849851-AccumulateVariantCallingMetrics-Picard 2020-04-02T18:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849871-CollectQualityYieldMetricsSpark-BETA 2020-04-02T19:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849891-CreateHadoopBamSplittingIndex-BETA 2020-04-02T19:02:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849911-PrintReads 2020-04-02T19:02:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849931-MateDistantReadFilter 2020-04-02T19:02:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849951-ValidAlignmentStartReadFilter 2020-04-02T19:02:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849971-ReadsPipelineSpark-BETA 2020-04-02T19:02:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360041849991-CountFalsePositives-BETA 2020-04-02T19:02:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850011-CollectIlluminaLaneMetrics-Picard 2020-04-02T19:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850031-SampleList 2020-04-02T18:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850051-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-04-02T19:02:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850071-CheckIlluminaDirectory-Picard 2020-04-02T19:02:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850091-CollectBaseDistributionByCycle-Picard 2020-04-02T18:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850111-MergeBamAlignment-Picard 2020-04-02T18:58:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850131-FixMisencodedBaseQualityReads 2020-04-02T19:02:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850151-LeftAlignAndTrimVariants 2020-04-02T19:02:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850171-ModelSegments 2020-04-02T18:58:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850191-RevertSamSpark-BETA 2020-04-02T19:02:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850211-RemoveNearbyIndels 2020-04-02T19:02:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850231-CompareDuplicatesSpark-BETA 2020-04-02T19:02:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850251-CollectRawWgsMetrics-Picard 2020-04-02T19:02:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850271-FilterByOrientationBias-EXPERIMENTAL 2020-04-02T19:02:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850291-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-04-02T18:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850311-PositionBasedDownsampleSam-Picard 2020-04-02T18:58:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850331-NotSupplementaryAlignmentReadFilter 2020-04-02T18:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850351-GenotypeSummaries 2020-04-02T18:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850371-FlagStatSpark 2020-04-02T19:02:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850391-PairedReadFilter 2020-04-02T18:58:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850411-GetPileupSummaries 2020-04-02T19:02:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850431-FifoBuffer-Picard 2020-04-02T18:58:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850451-ExcessHet 2020-04-02T18:58:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850471-VariantFiltration 2023-12-27T15:32:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850491-LikelihoodRankSumTest 2020-04-02T18:58:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850511-BaseRecalibrator 2020-04-02T19:02:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850531-RevertBaseQualityScores 2020-04-02T19:02:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850551-DownsampleSam-Picard 2020-04-02T19:02:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850571-PossibleDeNovo 2020-04-02T18:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850591-CollectInsertSizeMetricsSpark-BETA 2020-04-02T19:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850611-BaseQualityRankSumTest 2020-04-02T18:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850631-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-04-02T19:02:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850671-IntervalListToBed-Picard 2020-04-02T18:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850691-ApplyVQSR 2020-04-02T19:03:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850711-GermlineCNVCaller 2020-04-02T18:59:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850731-UpdateVcfSequenceDictionary-Picard 2020-04-02T18:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850751-ReadNameReadFilter 2020-04-02T18:59:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850771-MappingQualityZero 2020-04-02T19:03:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850791-CallCopyRatioSegments 2020-04-02T18:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850811-PlatformReadFilter 2020-04-02T18:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850831-BamIndexStats-Picard 2020-04-02T19:03:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850851-AddOrReplaceReadGroups-Picard 2020-04-02T18:59:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850871-CollectGcBiasMetrics-Picard 2020-04-02T18:59:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850891-LiftoverVcf-Picard 2020-04-02T19:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850911-AddOATag-Picard 2020-04-02T19:03:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850931-ReadPosition 2020-04-02T18:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850951-Coverage 2020-04-02T19:03:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041850991-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-04-02T18:59:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851011-CollectMultipleMetrics-Picard 2020-04-02T19:03:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851031-FlagStat 2020-04-02T19:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851051-CombineGenotypingArrayVcfs-Picard 2020-04-02T19:03:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851071-InbreedingCoeff 2020-04-02T18:59:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851091-FixMateInformation-Picard 2020-04-02T18:59:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851111-PrintVariantsSpark 2020-04-02T19:03:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851131-ValidateSamFile-Picard 2020-04-02T18:59:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851151-ReadGroupBlackListReadFilter 2020-04-02T18:59:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851171-CollectIlluminaBasecallingMetrics-Picard 2020-04-02T18:59:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851191-FuncotatorDataSourceDownloader 2020-04-02T18:59:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851211-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-04-02T18:59:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851231-CollectRnaSeqMetrics-Picard 2020-04-02T18:59:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851251-PathSeqScoreSpark 2020-04-02T19:03:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851271-RevertSam-Picard 2020-04-02T19:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851291-ReadPosRankSumTest 2020-04-02T18:59:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851311-BaseQuality 2020-04-02T18:59:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851331-SeqIsStoredReadFilter 2020-04-02T19:00:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851371-NonZeroReferenceLengthAlignmentReadFilter 2020-04-02T19:00:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851391-VariantRecalibrator 2020-04-23T18:15:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851411-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-04-02T19:03:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851451-SplitIntervals 2020-04-02T19:03:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851471-UnmarkDuplicates 2020-04-02T19:03:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851491-DepthOfCoverage-BETA 2021-09-09T15:43:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851511-ProperlyPairedReadFilter 2020-04-02T19:00:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851531-FilterFuncotations-EXPERIMENTAL 2020-04-02T19:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851551-TandemRepeat 2020-04-02T19:00:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851591-AnalyzeSaturationMutagenesis-BETA 2020-04-02T19:04:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851611-AS-QualByDepth 2020-04-02T19:04:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851651-Concordance 2020-04-02T19:04:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851671-FragmentLengthReadFilter 2020-04-02T19:00:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851711-BuildBamIndex-Picard 2020-04-02T19:04:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851731-CollectRrbsMetrics-Picard 2020-04-02T19:00:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851751-FindMendelianViolations-Picard 2020-04-02T19:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851771-IndexFeatureFile 2020-04-02T19:00:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851791-MetricsReadFilter 2020-04-02T19:00:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851811-ValidAlignmentEndReadFilter 2020-04-02T19:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851831-FastaReferenceMaker 2020-04-02T19:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851851-QualityScoreDistributionSpark-BETA 2020-04-02T19:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851871-DepthPerSampleHC 2020-04-02T19:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851891-AlleleFraction 2020-04-02T19:04:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851911-OrientationBiasReadCounts 2020-04-02T19:00:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851931-MappingQualityAvailableReadFilter 2020-04-02T19:00:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851951-CreateReadCountPanelOfNormals 2020-04-02T19:00:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851971-CollectDuplicateMetrics-Picard 2020-04-02T19:00:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360041851991-CountBasesSpark 2020-04-02T19:04:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360041852011-ASEReadCounter 2020-04-02T19:04:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360041852031-GtcToVcf-Picard 2020-04-02T19:00:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360041852051-CheckTerminatorBlock-Picard 2020-04-02T19:00:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360041852071-ReadLengthReadFilter 2020-04-02T19:00:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360041852091-CleanSam-Picard 2020-04-02T19:00:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360042106212-Genomics-in-the-Cloud-Origins 2020-06-30T12:03:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360042408831-Introducing-Genomics-in-the-Cloud-ie-The-GATK-book 2020-06-30T12:03:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475732-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2020-04-29T15:51:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475752-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2020-04-29T15:51:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475772-MeanQualityByCycle-Picard 2020-04-29T15:51:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475792-CollectHiSeqXPfFailMetrics-Picard 2020-04-29T15:51:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475812-GenotypeConcordance-Picard 2020-04-29T15:51:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475832-BwaMemIndexImageCreator 2020-04-29T15:51:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475852-NotProperlyPairedReadFilter 2020-04-29T15:46:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475872-SampleReadFilter 2020-04-29T15:46:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475892-RMSMappingQuality 2020-04-29T15:51:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475912-CollectQualityYieldMetrics-Picard 2020-04-29T15:46:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475932-CalcMetadataSpark-BETA 2020-04-29T15:51:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475952-FilterVcf-Picard 2020-04-29T15:47:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475972-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-04-29T15:51:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360042475992-AnnotatePairOrientation-EXPERIMENTAL 2020-04-29T15:51:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476012-FixVcfHeader-Picard 2020-04-29T15:51:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476032-GnarlyGenotyper-BETA 2020-04-29T15:51:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476052-PrintReadsHeader 2020-04-29T15:51:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476072-ViewSam-Picard 2020-04-29T15:51:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476092-CountVariants 2020-04-29T15:51:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476112-AllowAllReadsReadFilter 2020-04-29T15:47:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476132-LiftOverIntervalList-Picard 2020-04-29T15:47:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476152-NotDuplicateReadFilter 2020-04-29T15:47:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476172-VariantAnnotator 2020-04-29T15:51:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476192-FilterSamReads-Picard 2020-04-29T15:51:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476212-PrimaryLineReadFilter 2020-04-29T15:47:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476232-CollectMultipleMetricsSpark-BETA 2020-04-29T15:51:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476252-MappingQuality 2020-04-29T15:47:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476272-QualByDepth 2020-04-29T15:52:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476292-VariantsToTable 2020-04-29T15:52:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476312-AS-RMSMappingQuality 2020-04-29T15:52:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476332-CNNVariantWriteTensors-EXPERIMENTAL 2020-04-29T15:52:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476352-CountVariantsSpark 2020-04-29T15:52:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476372-UpdateVCFSequenceDictionary 2020-04-29T15:52:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476412-IlluminaBasecallsToFastq-Picard 2020-04-29T15:52:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476432-SamFormatConverter-Picard 2020-04-29T15:47:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476452-FisherStrand 2020-04-29T15:52:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476472-ClusterCrosscheckMetrics-Picard 2020-04-29T15:47:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476492-ClipReads 2020-04-29T15:52:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476512-CollectSamErrorMetrics-Picard 2020-04-29T15:47:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476532-SoftClippedReadFilter 2020-04-29T15:47:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476552-CalculateReadGroupChecksum-Picard 2020-04-29T15:52:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476572-SetNmMdAndUqTags-Picard 2020-04-29T15:52:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476592-CompareMetrics-Picard 2020-04-29T15:52:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476612-FuncotateSegments-BETA 2020-04-29T15:52:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476632-PathSeqBuildReferenceTaxonomy 2020-04-29T15:47:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476652-AS-FisherStrand 2020-04-29T15:52:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476672-CompareBaseQualities 2020-04-29T15:47:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476712-BwaSpark-BETA 2020-04-29T15:52:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476752-CollectAlignmentSummaryMetrics-Picard 2020-04-29T15:47:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476772-AnnotateVcfWithBamDepth 2020-04-29T15:52:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476792-GatherVcfs-Picard 2020-04-29T15:47:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476832-CalculateContamination 2020-04-29T15:52:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476852-ApplyBQSR 2020-04-29T15:52:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476892-CollectReadCounts 2020-04-29T15:52:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476912-MappingQualityNotZeroReadFilter 2020-04-29T15:48:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476932-CollectJumpingLibraryMetrics-Picard 2020-04-29T15:48:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476952-FilterMutectCalls 2020-04-29T15:52:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476972-BaseRecalibratorSpark-BETA 2020-04-29T15:52:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042476992-IlluminaBasecallsToSam-Picard 2020-04-29T15:52:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477032-MappingQualityReadFilter 2020-04-29T15:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477052-GenomicsDBImport 2020-04-29T15:52:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477072-PlatformUnitReadFilter 2020-04-29T15:48:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477092-CreateHadoopBamSplittingIndex-BETA 2020-04-29T15:52:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477112-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-04-29T15:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477132-ReadsPipelineSpark-BETA 2020-04-29T15:52:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477152-MateUnmappedAndUnmappedReadFilter 2020-04-29T15:48:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477172-CollectIlluminaLaneMetrics-Picard 2020-04-29T15:52:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477212-PathSeqBwaSpark 2020-04-29T15:52:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477232-SampleList 2020-04-29T15:48:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477252-MatchingBasesAndQualsReadFilter 2020-04-29T15:48:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477272-MeanQualityByCycleSpark-BETA 2020-04-29T15:52:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477292-FragmentLength 2020-04-29T15:48:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477312-CollectBaseDistributionByCycle-Picard 2020-04-29T15:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477332-ReblockGVCF-BETA 2020-04-29T15:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477372-ExtractIlluminaBarcodes-Picard 2020-04-29T15:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477392-AmbiguousBaseReadFilter 2020-04-29T15:48:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477412-BedToIntervalList-Picard 2020-04-29T15:53:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477432-RemoveNearbyIndels 2020-04-29T15:53:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477452-CollectRawWgsMetrics-Picard 2020-04-29T15:53:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477472-FilterByOrientationBias-EXPERIMENTAL 2020-04-29T15:53:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477492-MarkDuplicates-Picard 2020-04-29T15:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477512-GoodCigarReadFilter 2020-04-29T15:49:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477532-PositionBasedDownsampleSam-Picard 2020-04-29T15:49:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477552-ReorderSam-Picard 2020-04-29T15:49:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477572-PostprocessGermlineCNVCalls 2020-04-29T15:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477592-NotSupplementaryAlignmentReadFilter 2020-04-29T15:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477612-FilterAlignmentArtifacts-EXPERIMENTAL 2020-04-29T15:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477632-CollectWgsMetrics-Picard 2020-04-29T15:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477652-VariantFiltration 2020-04-29T15:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477672-BaseRecalibrator 2020-04-29T15:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477692-RevertBaseQualityScores 2020-04-29T15:53:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477712-CompareSAMs-Picard 2020-04-29T15:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477732-PossibleDeNovo 2020-04-29T15:49:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477752-DenoiseReadCounts 2020-04-29T15:49:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477772-BaseQualityRankSumTest 2020-04-29T15:49:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477792-ApplyVQSR 2020-04-29T15:53:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477812-GermlineCNVCaller 2020-06-23T09:28:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477832-UpdateVcfSequenceDictionary-Picard 2020-04-29T15:49:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477852-ReadNameReadFilter 2020-04-29T15:49:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477872-CallCopyRatioSegments 2020-04-29T15:49:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477892-ScatterIntervalsByNs-Picard 2020-04-29T15:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477912-AS-InbreedingCoeff 2020-04-29T15:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477932-PlatformReadFilter 2020-04-29T15:49:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477952-Mutect2 2020-04-29T15:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477972-CollectArraysVariantCallingMetrics-Picard 2020-04-29T15:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360042477992-PlotModeledSegments 2021-04-28T04:16:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478012-CollectVariantCallingMetrics-Picard 2020-04-29T15:49:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478052-ReadPosition 2020-04-29T15:49:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478072-MateOnSameContigOrNoMappedMateReadFilter 2020-04-29T15:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478092-ApplyBQSRSpark-BETA 2020-04-29T15:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478112-CollectMultipleMetrics-Picard 2020-04-29T15:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478132-ExtractSVEvidenceSpark-BETA 2020-04-29T15:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478152-CollectAllelicCounts 2020-04-29T15:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478172-QualityScoreDistribution-Picard 2020-04-29T15:50:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478192-BaitDesigner-Picard 2020-04-29T15:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478212-InbreedingCoeff 2020-04-29T15:50:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478272-ValidateSamFile-Picard 2020-04-29T15:50:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478292-SamToFastq-Picard 2020-04-29T15:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478312-CollectIlluminaBasecallingMetrics-Picard 2020-04-29T15:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478332-FuncotatorDataSourceDownloader 2020-04-29T15:50:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478352-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-04-29T15:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478372-CollectRnaSeqMetrics-Picard 2020-04-29T15:50:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478392-GatherVcfsCloud-BETA 2020-04-29T15:54:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478412-AnnotateIntervals 2020-04-29T15:54:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478452-PassesVendorQualityCheckReadFilter 2020-04-29T15:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478472-FixCallSetSampleOrdering-EXPERIMENTAL 2020-04-29T15:54:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478492-SeqIsStoredReadFilter 2020-04-29T15:50:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478512-IntervalOverlapReadFilter 2020-04-29T15:50:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478532-PathSeqFilterSpark 2020-04-29T15:54:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478552-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-04-29T15:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478572-PlotDenoisedCopyRatios 2020-04-29T15:50:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478592-SplitIntervals 2020-04-29T15:54:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478612-UnmarkDuplicates 2020-04-29T15:54:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478632-EvaluateInfoFieldConcordance-BETA 2020-04-29T15:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478652-SplitNCigarReads 2020-04-29T15:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478672-ProperlyPairedReadFilter 2020-04-29T15:50:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478692-FilterFuncotations-EXPERIMENTAL 2020-04-29T15:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478712-SplitSamByLibrary-Picard 2020-04-29T15:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478732-CNNVariantTrain-EXPERIMENTAL 2020-04-29T15:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478752-FindBadGenomicKmersSpark-BETA 2020-04-29T15:54:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478772-AnalyzeSaturationMutagenesis-BETA 2020-04-29T15:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478812-AS-QualByDepth 2020-04-29T15:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478832-FragmentLengthReadFilter 2020-04-29T15:50:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478852-BuildBamIndex-Picard 2020-04-29T15:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478872-CollectRrbsMetrics-Picard 2020-04-29T15:51:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478892-ReferenceBases 2020-04-29T15:51:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478912-MetricsReadFilter 2020-04-29T15:51:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478932-ValidAlignmentEndReadFilter 2020-04-29T15:54:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478952-QualityScoreDistributionSpark-BETA 2020-04-29T15:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042478972-DepthPerSampleHC 2020-04-29T15:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479012-CollectOxoGMetrics-Picard 2020-04-29T15:51:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479032-CountBasesSpark 2020-04-29T15:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479052-PrintReadsSpark 2020-04-29T15:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479072-ASEReadCounter 2020-04-29T15:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479092-FilterVariantTranches 2020-04-29T15:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479112-CreateSomaticPanelOfNormals-BETA 2021-01-23T09:30:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479132-CheckPileup 2020-04-29T15:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479152-GtcToVcf-Picard 2020-04-29T15:51:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479172-CheckTerminatorBlock-Picard 2020-04-29T15:51:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360042479192-ReadLengthReadFilter 2020-04-29T15:51:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911851-ChromosomeCounts 2020-04-29T15:46:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911871-LibraryReadFilter 2020-04-29T15:46:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911891-NonChimericOriginalAlignmentReadFilter 2020-04-29T15:46:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911911-Pileup 2020-04-29T15:51:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911931-OverclippedReadFilter 2020-04-29T15:46:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911951-WellformedReadFilter 2020-04-29T15:51:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911971-AnalyzeCovariates 2020-04-29T15:51:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360042911991-FirstOfPairReadFilter 2020-04-29T15:46:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912011-Funcotator 2023-05-02T15:13:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912031-PathSeqPipelineSpark 2020-04-29T15:51:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912051-SecondOfPairReadFilter 2020-04-29T15:46:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912071-AlignmentAgreesWithHeaderReadFilter 2020-04-29T15:47:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912091-AS-StrandOddsRatio 2020-04-29T15:51:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912111-VariantEval-BETA 2020-04-29T15:51:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912131-CountReads 2020-04-29T15:51:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912151-CollectHsMetrics-Picard 2020-05-18T18:44:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912171-EstimateLibraryComplexity-Picard 2020-04-29T15:51:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912211-AnnotateVcfWithExpectedAlleleFraction 2020-04-29T15:51:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912231-BamToBfq-Picard 2020-04-29T15:47:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912251-MergePedIntoVcf-Picard 2020-04-29T15:47:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912271-CountBases 2020-04-29T15:51:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912291-StrandOddsRatio 2020-04-29T15:51:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912311--Tool-Documentation-Index 2020-04-29T23:21:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912331-CheckFingerprint-Picard 2020-04-29T15:47:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912351-HasReadGroupReadFilter 2020-04-29T15:47:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912371-DetermineGermlineContigPloidy 2020-04-29T15:47:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912391-FindBreakpointEvidenceSpark-BETA 2020-04-29T15:51:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912411-UniqueAltReadCount 2020-04-29T15:47:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912431-NormalizeFasta-Picard 2020-04-29T15:52:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912491-GetSampleName 2020-04-29T15:52:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912511-MarkDuplicatesSpark 2020-04-29T15:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912531-DepthPerAlleleBySample 2020-04-29T15:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912551-GatherBamFiles-Picard 2020-04-29T15:47:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912591-CalculateFingerprintMetrics-Picard 2020-04-29T15:47:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912631-CollectSequencingArtifactMetrics-Picard 2020-04-29T15:47:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912651-MappedReadFilter 2020-04-29T15:47:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912671-ExtractSequences-Picard 2020-04-29T15:52:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912691-MarkDuplicatesWithMateCigar-Picard 2020-04-29T15:52:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912711-AlleleFrequency 2020-04-29T15:47:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912731-GatherBQSRReports 2020-04-29T15:47:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912751-CpxVariantReInterpreterSpark-BETA 2020-04-29T15:52:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912771-PathSeqBuildKmers 2020-04-29T15:52:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912791-MakeSitesOnlyVcf-Picard 2020-04-29T15:52:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912811-IntervalListTools-Picard 2020-04-29T15:52:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912831-CollectInsertSizeMetrics-Picard 2020-04-29T15:48:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912851-StrandBiasBySample 2020-04-29T15:52:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912871-SortSamSpark-BETA 2020-04-29T15:52:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912891-LeftAlignIndels 2020-04-29T15:52:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912931-FilterIntervals 2020-04-29T15:48:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912951-MappingQualityRankSumTest 2020-04-29T15:52:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912971-HaplotypeCallerSpark-BETA 2020-04-29T15:52:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360042912991-SplitSamByNumberOfReads-Picard 2020-04-29T15:52:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913011-MateDifferentStrandReadFilter 2020-04-29T15:52:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913031-NonNFastaSize-Picard 2020-04-29T15:52:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913051-CalculateMixingFractions 2020-04-29T15:52:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913071-SelectVariants 2020-04-29T15:52:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913091-AccumulateVariantCallingMetrics-Picard 2020-04-29T15:48:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913111-ReadGroupReadFilter 2020-04-29T15:48:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913131-CollectQualityYieldMetricsSpark-BETA 2020-04-29T15:52:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913171-PrintReads 2020-04-29T15:52:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913191-MateDistantReadFilter 2020-04-29T15:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913231-HaplotypeCaller 2024-06-06T07:41:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913251-ValidAlignmentStartReadFilter 2020-04-29T15:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913271-ReplaceSamHeader-Picard 2020-04-29T15:52:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913291-CountFalsePositives-BETA 2020-04-29T15:52:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913311-CountBasesInReference 2020-04-29T15:52:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913331-VcfToIntervalList-Picard 2020-04-29T15:52:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913351-SetNmAndUqTags-Picard 2020-04-29T15:52:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913371-MarkIlluminaAdapters-Picard 2020-04-29T15:52:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913391-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-04-29T15:52:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913431-CheckIlluminaDirectory-Picard 2020-04-29T15:52:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913451-CollectTargetedPcrMetrics-Picard 2020-04-29T15:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913471-MergeBamAlignment-Picard 2020-04-29T15:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913491-FixMisencodedBaseQualityReads 2020-04-29T15:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913511-LeftAlignAndTrimVariants 2020-04-29T15:53:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913531-ModelSegments 2020-04-29T15:48:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913551-RevertSamSpark-BETA 2020-04-29T15:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913571-CompareDuplicatesSpark-BETA 2020-04-29T15:53:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913591-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-04-29T15:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913611-OriginalAlignment 2020-04-29T15:49:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913631-CreateSequenceDictionary-Picard 2020-04-29T15:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913651-VcfToAdpc-Picard 2020-04-29T15:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913671-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-04-29T15:49:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913691-GenotypeSummaries 2020-04-29T15:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913711-FlagStatSpark 2020-04-29T15:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913731-PairedReadFilter 2020-04-29T15:49:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913751-AS-ReadPosRankSumTest 2020-04-29T15:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913771-GetPileupSummaries 2020-04-29T15:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913791-FifoBuffer-Picard 2020-04-29T15:49:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913811-ExcessHet 2020-04-29T15:49:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913831-LikelihoodRankSumTest 2020-04-29T15:49:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913871-GatherTranches-BETA 2020-04-29T15:49:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913891-DownsampleSam-Picard 2020-04-29T15:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913911-ClippingRankSumTest 2020-04-29T15:49:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913931-BQSRPipelineSpark-BETA 2020-04-29T15:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913951-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-04-29T15:53:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913971-CollectInsertSizeMetricsSpark-BETA 2020-04-29T15:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360042913991-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-04-29T15:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914011-IntervalListToBed-Picard 2020-04-29T15:49:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914031-MappingQualityZero 2020-04-29T15:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914051-BamIndexStats-Picard 2020-04-29T15:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914071-VcfFormatConverter-Picard 2020-04-29T15:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914091-AddOrReplaceReadGroups-Picard 2020-04-29T15:49:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914111-CombineGVCFs 2020-04-29T15:53:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914131-CollectGcBiasMetrics-Picard 2020-04-29T15:49:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914151-LiftoverVcf-Picard 2020-04-29T15:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914171-AddOATag-Picard 2020-04-29T15:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914191-Coverage 2020-04-29T15:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914211-ReadStrandFilter 2020-04-29T15:49:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914231-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-04-29T15:49:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914251-CalculateGenotypePosteriors 2020-04-29T15:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914271-MergeVcfs-Picard 2020-04-29T15:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914291-ValidateVariants 2020-04-29T15:53:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914311-CNNScoreVariants 2020-04-29T15:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914351-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-04-29T15:50:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914371-MethylationTypeCaller-EXPERIMENTAL 2020-04-29T15:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914391-PreprocessIntervals 2020-04-29T15:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914411-FlagStat 2020-04-29T15:53:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914431-CombineGenotypingArrayVcfs-Picard 2020-04-29T15:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914451-ReadLengthEqualsCigarLengthReadFilter 2020-04-29T15:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914471-FixMateInformation-Picard 2020-04-29T15:50:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914491-SortVcf-Picard 2020-04-29T15:54:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914511-PrintVariantsSpark 2020-04-29T15:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914531-FastqToSam-Picard 2020-04-29T15:54:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914551-ReadGroupBlackListReadFilter 2020-04-29T15:50:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914571-SortSam-Picard 2020-04-29T15:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914591-MergeSamFiles-Picard 2020-04-29T15:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914611-PathSeqScoreSpark 2020-04-29T15:54:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914631-RevertSam-Picard 2020-04-29T15:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914651-SplitReads 2020-04-29T15:54:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914671-AS-MappingQualityRankSumTest 2020-04-29T15:54:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914711-ReadPosRankSumTest 2020-04-29T15:50:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914731-BaseQuality 2020-04-29T15:50:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914751-NonZeroReferenceLengthAlignmentReadFilter 2020-04-29T15:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914771-CollectBaseDistributionByCycleSpark-BETA 2020-04-29T15:54:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914791-VariantRecalibrator 2021-01-14T10:05:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914811-FastaAlternateReferenceMaker 2020-04-29T15:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914831-StructuralVariationDiscoveryPipelineSpark-BETA 2021-11-02T20:03:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914851-NonZeroFragmentLengthReadFilter 2020-04-29T15:50:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914871-DepthOfCoverage-BETA 2020-05-05T21:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914891-PileupSpark-BETA 2020-04-29T15:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914911-CigarContainsNoNOperator 2020-04-29T15:50:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914931-SplitVcfs-Picard 2020-04-29T15:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914971-CrosscheckFingerprints-Picard 2020-04-29T15:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360042914991-GenotypeGVCFs 2020-04-29T15:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915011-TandemRepeat 2020-04-29T15:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915031-AddCommentsToBam-Picard 2020-04-29T15:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915051-AS-BaseQualityRankSumTest 2020-04-29T15:54:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915071-Concordance 2020-04-29T15:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915091-NotSecondaryAlignmentReadFilter 2020-04-29T15:51:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915131-FindMendelianViolations-Picard 2020-04-29T15:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915151-IndexFeatureFile 2020-04-29T15:51:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915171-FastaReferenceMaker 2020-04-29T15:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915211-AlleleFraction 2020-04-29T15:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915231-ConvertSequencingArtifactToOxoG-Picard 2020-04-29T15:51:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915251-OrientationBiasReadCounts 2020-04-29T15:51:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915271-CountNs 2020-04-29T15:51:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915291-RenameSampleInVcf-Picard 2020-04-29T15:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915311-MappingQualityAvailableReadFilter 2020-04-29T15:51:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915351-CreateReadCountPanelOfNormals 2020-04-29T15:51:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915371-CollectDuplicateMetrics-Picard 2020-04-29T15:51:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915391-CountReadsSpark 2020-04-29T15:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360042915411-CleanSam-Picard 2020-04-29T15:51:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant 2024-06-25T07:16:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360045673592--GATK-4-1-8-0-release 2024-07-01T17:20:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360045763652-Where-can-I-get-the-GATK-source-code-Is-it-open-source 2024-06-25T07:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798392-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2020-07-14T13:23:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798412-ChromosomeCounts 2020-07-14T13:18:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798432-LibraryReadFilter 2020-07-14T13:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798452-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2020-07-14T13:18:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798472-MeanQualityByCycle-Picard 2020-07-14T13:23:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798492-GenotypeConcordance-Picard 2020-07-14T13:23:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798512-Pileup 2020-07-14T13:23:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798532-BwaMemIndexImageCreator 2020-07-14T13:23:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798552-RMSMappingQuality 2020-07-14T13:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798572-FirstOfPairReadFilter 2020-07-14T13:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798592-Funcotator 2020-08-12T02:52:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798612-CollectQualityYieldMetrics-Picard 2020-07-14T13:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798632-CalcMetadataSpark-BETA 2020-07-14T13:23:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798652-AS-StrandOddsRatio 2020-07-14T13:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798672-AnnotatePairOrientation-EXPERIMENTAL 2020-07-14T13:23:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798692-VariantEval-BETA 2020-07-14T13:19:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798712-CountReads 2020-07-14T13:23:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798732-FixVcfHeader-Picard 2020-07-14T13:23:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798752-CollectHsMetrics-Picard 2020-07-14T13:23:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798772-EstimateLibraryComplexity-Picard 2020-07-14T13:19:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798792-CountVariants 2020-07-14T13:24:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798832-AllowAllReadsReadFilter 2020-07-14T13:19:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798852-NotDuplicateReadFilter 2020-07-14T13:19:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798872-BamToBfq-Picard 2020-07-14T13:19:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798892-FilterSamReads-Picard 2020-07-14T13:24:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798912-PrimaryLineReadFilter 2020-07-14T13:19:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798932-CountBases 2020-07-14T13:24:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798952-StrandOddsRatio 2020-07-14T13:19:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798972--Tool-Documentation-Index 2020-07-14T13:24:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360045798992-HasReadGroupReadFilter 2020-07-14T13:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799012-DetermineGermlineContigPloidy 2020-07-14T13:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799032-FindBreakpointEvidenceSpark-BETA 2020-07-14T13:24:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799052-UniqueAltReadCount 2020-07-14T13:19:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799072-NormalizeFasta-Picard 2020-07-14T13:24:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799092-CNNVariantWriteTensors-EXPERIMENTAL 2020-07-14T13:24:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799112-UpdateVCFSequenceDictionary 2020-07-14T13:24:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799132-IlluminaBasecallsToFastq-Picard 2020-07-14T13:19:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799172-FisherStrand 2020-07-14T13:19:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799192-ClipReads 2020-07-14T13:24:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799212-CollectSamErrorMetrics-Picard 2020-07-14T13:19:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799232-SoftClippedReadFilter 2020-07-14T13:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799252-SetNmMdAndUqTags-Picard 2020-07-14T13:24:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799292-FuncotateSegments-BETA 2020-07-14T13:24:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799312-GatherBamFiles-Picard 2020-07-14T13:19:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799332-CalculateFingerprintMetrics-Picard 2020-07-14T13:19:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799352-AS-FisherStrand 2020-07-14T13:19:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799372-CompareBaseQualities 2020-07-14T13:19:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799392-BwaSpark-BETA 2020-07-14T13:24:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799412-CollectAlignmentSummaryMetrics-Picard 2020-07-14T13:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799432-AnnotateVcfWithBamDepth 2020-07-14T13:24:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799452-CollectSequencingArtifactMetrics-Picard 2020-07-14T13:19:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799472-ExtractSequences-Picard 2020-07-14T13:24:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799492-AlleleFrequency 2020-07-14T13:19:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799512-GatherBQSRReports 2020-07-14T13:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799532-CpxVariantReInterpreterSpark-BETA 2020-07-14T13:24:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799552-MakeSitesOnlyVcf-Picard 2020-07-14T13:24:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799572-CollectInsertSizeMetrics-Picard 2020-07-14T13:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799592-CollectReadCounts 2020-07-14T13:24:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799612-SortSamSpark-BETA 2020-07-14T13:24:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799632-MappingQualityRankSumTest 2020-07-14T13:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799652-MappingQualityNotZeroReadFilter 2020-07-14T13:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799672-CollectJumpingLibraryMetrics-Picard 2020-07-14T13:20:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799692-NonNFastaSize-Picard 2020-07-14T13:24:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799712-FilterMutectCalls 2020-07-14T13:24:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799732-BaseRecalibratorSpark-BETA 2020-07-14T13:24:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799752-SelectVariants 2020-07-14T13:24:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799772-AccumulateVariantCallingMetrics-Picard 2020-07-14T13:20:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799792-MappingQualityReadFilter 2020-07-14T13:24:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799812-CollectQualityYieldMetricsSpark-BETA 2020-07-14T13:24:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799832-CreateHadoopBamSplittingIndex-BETA 2020-07-14T13:20:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799852-PrintReads 2020-07-14T13:24:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799872-MateDistantReadFilter 2020-07-14T13:24:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799892-HaplotypeCaller 2020-07-14T13:24:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799912-ValidAlignmentStartReadFilter 2020-07-14T13:25:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799932-ReadsPipelineSpark-BETA 2020-07-14T13:25:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799952-CountFalsePositives-BETA 2020-07-14T13:25:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799972-MateUnmappedAndUnmappedReadFilter 2020-07-14T13:20:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360045799992-CollectIlluminaLaneMetrics-Picard 2020-07-14T13:20:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800012-SetNmAndUqTags-Picard 2020-07-14T13:25:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800032-PathSeqBwaSpark 2020-07-14T13:25:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800052-MarkIlluminaAdapters-Picard 2020-07-14T13:25:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800072-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-07-14T13:25:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800092-CollectTargetedPcrMetrics-Picard 2020-07-14T13:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800112-ReblockGVCF-BETA 2020-07-14T13:25:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800132-FixMisencodedBaseQualityReads 2020-07-14T13:25:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800152-BedToIntervalList-Picard 2020-07-14T13:25:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800172-GoodCigarReadFilter 2020-07-14T13:21:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800192-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-07-14T13:21:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800212-PositionBasedDownsampleSam-Picard 2020-07-14T13:21:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800232-CollectWgsMetrics-Picard 2020-07-14T13:21:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800252-PairedReadFilter 2020-07-14T13:21:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800272-GetPileupSummaries 2020-07-14T13:25:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800292-FifoBuffer-Picard 2020-07-14T13:21:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800312-ExcessHet 2020-07-14T13:21:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800332-VariantFiltration 2020-07-14T13:25:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800352-GatherTranches-BETA 2020-07-14T13:21:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800372-DownsampleSam-Picard 2020-07-14T13:25:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800412-ClippingRankSumTest 2020-07-14T13:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800432-CompareSAMs-Picard 2020-07-14T13:25:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800452-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-07-14T13:25:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800472-DenoiseReadCounts 2020-07-14T13:21:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800492-IntervalListToBed-Picard 2020-07-14T13:21:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800512-ApplyVQSR 2020-07-14T13:25:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800532-AS-InbreedingCoeff 2020-07-14T13:21:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800552-Mutect2 2020-07-31T18:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800572-CollectArraysVariantCallingMetrics-Picard 2020-07-14T13:25:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800592-CombineGVCFs 2020-07-14T13:25:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800612-CollectGcBiasMetrics-Picard 2020-07-14T13:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800632-LiftoverVcf-Picard 2020-07-14T13:25:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800652-AddOATag-Picard 2020-07-14T13:25:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800672-Coverage 2020-07-14T13:21:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800692-ReadStrandFilter 2020-07-14T13:21:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800712-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-07-14T13:22:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800732-MergeVcfs-Picard 2020-07-14T13:26:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800752-ValidateVariants 2020-07-14T13:26:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800772-CNNScoreVariants 2020-07-23T16:36:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800792-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-07-14T13:22:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800812-PreprocessIntervals 2020-07-14T13:26:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800832-CombineGenotypingArrayVcfs-Picard 2020-07-14T13:26:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800852-BaitDesigner-Picard 2020-07-14T13:26:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800872-InbreedingCoeff 2020-07-14T13:22:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800892-ReadLengthEqualsCigarLengthReadFilter 2020-07-14T13:26:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800912-FixMateInformation-Picard 2020-07-14T13:22:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800932-SortVcf-Picard 2020-07-14T13:26:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800952-ValidateSamFile-Picard 2020-07-14T13:22:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800972-FastqToSam-Picard 2020-07-14T13:26:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360045800992-CollectIlluminaBasecallingMetrics-Picard 2020-07-14T13:22:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801012-FuncotatorDataSourceDownloader 2020-07-14T13:22:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801032-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-07-14T13:22:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801052-CollectRnaSeqMetrics-Picard 2020-07-14T13:22:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801092-PathSeqScoreSpark 2020-07-14T13:26:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801112-IntervalOverlapReadFilter 2020-07-14T13:22:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801132-NonZeroReferenceLengthAlignmentReadFilter 2020-07-14T13:22:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801152-CollectBaseDistributionByCycleSpark-BETA 2020-07-14T13:26:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801172-FastaAlternateReferenceMaker 2020-07-14T13:26:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801192-StructuralVariationDiscoveryPipelineSpark-BETA 2020-07-14T13:26:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801212-SplitNCigarReads 2020-07-14T13:26:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801232-NonZeroFragmentLengthReadFilter 2020-07-14T13:22:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801252-ProperlyPairedReadFilter 2020-07-14T13:22:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801272-CigarContainsNoNOperator 2020-07-14T13:22:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801292-CrosscheckFingerprints-Picard 2020-07-14T13:26:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801312-FindBadGenomicKmersSpark-BETA 2020-07-14T13:26:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801332-AddCommentsToBam-Picard 2020-07-14T13:26:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801352-AS-QualByDepth 2020-07-14T13:26:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801372-Concordance 2020-07-14T13:26:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801392-BuildBamIndex-Picard 2020-07-14T13:26:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801412-FindMendelianViolations-Picard 2020-07-14T13:26:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801432-ReferenceBases 2020-07-14T13:23:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801452-IndexFeatureFile 2020-07-14T13:23:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801472-MetricsReadFilter 2020-07-14T13:23:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801492-FastaReferenceMaker 2020-07-14T13:26:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801512-AlleleFraction 2020-07-14T13:23:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801532-ConvertSequencingArtifactToOxoG-Picard 2020-07-14T13:23:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801552-OrientationBiasReadCounts 2020-07-14T13:23:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801572-CountNs 2020-07-14T13:23:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801592-RenameSampleInVcf-Picard 2020-07-14T13:26:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801612-CountReadsSpark 2020-07-14T13:27:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801632-ASEReadCounter 2020-07-14T13:27:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801652-FilterVariantTranches 2020-07-14T13:27:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360045801672-CheckTerminatorBlock-Picard 2020-07-14T13:23:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360045944831-DRAGEN-GATK 2024-07-15T05:43:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221191-NonChimericOriginalAlignmentReadFilter 2020-07-14T13:18:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221211-CollectHiSeqXPfFailMetrics-Picard 2020-07-14T13:18:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221231-OverclippedReadFilter 2020-07-14T13:18:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221251-NotProperlyPairedReadFilter 2020-07-14T13:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221271-WellformedReadFilter 2020-07-14T13:23:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221291-SampleReadFilter 2020-07-14T13:18:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221311-AnalyzeCovariates 2020-07-14T13:23:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221351-PathSeqPipelineSpark 2020-07-14T13:23:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221371-SecondOfPairReadFilter 2020-07-14T13:18:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221391-AlignmentAgreesWithHeaderReadFilter 2020-07-14T13:18:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221431-FilterVcf-Picard 2020-07-14T13:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221451-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-07-14T13:23:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221471-GnarlyGenotyper-BETA 2020-07-14T13:23:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221491-PrintReadsHeader 2020-07-14T13:23:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221511-ViewSam-Picard 2020-07-14T13:23:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221531-AnnotateVcfWithExpectedAlleleFraction 2020-07-14T13:23:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221551-LiftOverIntervalList-Picard 2020-07-14T13:19:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221571-VariantAnnotator 2020-07-14T13:24:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221591-MergePedIntoVcf-Picard 2020-07-14T13:19:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221611-CollectMultipleMetricsSpark-BETA 2020-07-14T13:24:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221631-CheckFingerprint-Picard 2020-07-14T13:19:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221651-MappingQuality 2020-07-14T13:19:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221671-QualByDepth 2020-07-14T13:19:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221691-VariantsToTable 2020-07-14T13:24:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221711-AS-RMSMappingQuality 2020-07-14T13:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221731-CountVariantsSpark 2020-07-14T13:19:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221751-SamFormatConverter-Picard 2020-07-14T13:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221771-ClusterCrosscheckMetrics-Picard 2020-07-14T13:19:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221791-GetSampleName 2020-07-14T13:24:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221811-MarkDuplicatesSpark 2020-07-14T13:24:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221831-DepthPerAlleleBySample 2020-07-14T13:19:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221851-CalculateReadGroupChecksum-Picard 2020-07-14T13:24:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221871-CompareMetrics-Picard 2020-07-14T13:24:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221891-PathSeqBuildReferenceTaxonomy 2020-07-14T13:19:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221931-GatherVcfs-Picard 2020-07-14T13:19:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221951-MappedReadFilter 2020-07-14T13:19:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221971-MarkDuplicatesWithMateCigar-Picard 2020-07-14T13:24:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360046221991-CalculateContamination 2020-07-14T13:24:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222011-ApplyBQSR 2020-07-14T13:24:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222031-PathSeqBuildKmers 2020-07-14T13:24:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222051-IntervalListTools-Picard 2020-07-14T13:24:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222071-StrandBiasBySample 2020-07-14T13:20:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222091-LeftAlignIndels 2020-07-14T13:24:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222111-FilterIntervals 2020-07-14T13:20:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222131-HaplotypeCallerSpark-BETA 2020-07-14T13:24:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222151-SplitSamByNumberOfReads-Picard 2020-07-14T13:24:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222171-MateDifferentStrandReadFilter 2020-07-14T13:24:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222191-CalculateMixingFractions 2020-07-14T13:24:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222211-IlluminaBasecallsToSam-Picard 2020-07-14T13:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222231-ReadGroupReadFilter 2020-07-14T13:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222251-GenomicsDBImport 2020-08-01T09:15:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222271-PlatformUnitReadFilter 2020-07-14T13:20:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222291-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-07-14T13:24:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222311-ReplaceSamHeader-Picard 2020-07-14T13:25:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222331-CountBasesInReference 2020-07-14T13:25:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222351-VcfToIntervalList-Picard 2020-07-14T13:25:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222391-SampleList 2020-07-14T13:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222411-MatchingBasesAndQualsReadFilter 2020-07-14T13:20:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222431-MeanQualityByCycleSpark-BETA 2020-07-14T13:25:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222451-FragmentLength 2020-07-14T13:20:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222471-CheckIlluminaDirectory-Picard 2020-07-14T13:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222491-CollectBaseDistributionByCycle-Picard 2020-07-14T13:20:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222511-MergeBamAlignment-Picard 2020-07-14T13:20:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222531-LeftAlignAndTrimVariants 2020-07-14T13:25:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222551-ModelSegments 2020-07-14T13:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222571-RevertSamSpark-BETA 2020-07-14T13:25:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222591-ExtractIlluminaBarcodes-Picard 2020-07-14T13:20:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222611-AmbiguousBaseReadFilter 2020-07-14T13:20:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222631-RemoveNearbyIndels 2020-07-14T13:25:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222651-CompareDuplicatesSpark-BETA 2020-07-14T13:25:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222671-CollectRawWgsMetrics-Picard 2020-07-14T13:25:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222691-FilterByOrientationBias-EXPERIMENTAL 2020-07-14T13:25:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222711-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-07-14T13:25:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222731-OriginalAlignment 2020-07-14T13:21:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222751-MarkDuplicates-Picard 2020-07-14T13:21:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222771-CreateSequenceDictionary-Picard 2020-07-14T13:25:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222791-VcfToAdpc-Picard 2020-07-14T13:21:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222811-ReorderSam-Picard 2020-07-14T13:21:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222831-PostprocessGermlineCNVCalls 2020-07-14T13:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222851-NotSupplementaryAlignmentReadFilter 2020-07-14T13:21:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222871-GenotypeSummaries 2020-07-14T13:21:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222891-FlagStatSpark 2020-07-14T13:25:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222911-FilterAlignmentArtifacts-EXPERIMENTAL 2020-07-14T13:25:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222931-AS-ReadPosRankSumTest 2020-07-14T13:21:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222971-LikelihoodRankSumTest 2020-07-14T13:21:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046222991-BaseRecalibrator 2020-07-14T13:25:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223011-RevertBaseQualityScores 2020-07-14T13:25:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223031-BQSRPipelineSpark-BETA 2020-07-14T13:25:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223051-PossibleDeNovo 2020-07-14T13:21:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223071-CollectInsertSizeMetricsSpark-BETA 2020-07-14T13:25:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223091-BaseQualityRankSumTest 2020-07-14T13:21:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223111-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-07-14T13:25:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223131-GermlineCNVCaller 2020-07-14T13:21:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223151-UpdateVcfSequenceDictionary-Picard 2020-07-14T13:21:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223171-ReadNameReadFilter 2020-07-14T13:21:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223211-MappingQualityZero 2020-07-14T13:21:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223231-CallCopyRatioSegments 2020-07-14T13:21:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223251-ScatterIntervalsByNs-Picard 2020-07-14T13:25:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223271-PlatformReadFilter 2020-07-14T13:21:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223291-BamIndexStats-Picard 2020-07-14T13:25:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223311-VcfFormatConverter-Picard 2020-07-14T13:25:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223331-AddOrReplaceReadGroups-Picard 2020-07-14T13:21:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223351-PlotModeledSegments 2020-07-14T13:21:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223371-CollectVariantCallingMetrics-Picard 2020-07-14T13:21:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223391-ReadPosition 2020-07-14T13:21:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223411-MateOnSameContigOrNoMappedMateReadFilter 2020-07-14T13:25:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223431-ApplyBQSRSpark-BETA 2020-07-14T13:26:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223451-CalculateGenotypePosteriors 2020-07-14T13:26:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223471-CollectMultipleMetrics-Picard 2020-07-14T13:26:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223491-ExtractSVEvidenceSpark-BETA 2020-07-14T13:26:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223511-CollectAllelicCounts 2020-07-14T13:26:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223531-MethylationTypeCaller-EXPERIMENTAL 2020-07-14T13:26:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223551-QualityScoreDistribution-Picard 2020-07-14T13:22:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223571-FlagStat 2020-07-14T13:26:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223591-PrintVariantsSpark 2020-07-14T13:26:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223611-ReadGroupBlackListReadFilter 2020-07-14T13:22:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223631-SamToFastq-Picard 2020-07-14T13:26:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223651-SortSam-Picard 2020-07-14T13:26:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223671-MergeSamFiles-Picard 2020-07-14T13:26:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223691-GatherVcfsCloud-BETA 2020-07-14T13:22:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223711-AnnotateIntervals 2020-07-14T13:26:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223731-RevertSam-Picard 2020-07-14T13:26:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223751-PassesVendorQualityCheckReadFilter 2020-07-14T13:22:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223771-SplitReads 2020-07-14T13:26:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223791-AS-MappingQualityRankSumTest 2020-07-14T13:22:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223811-FixCallSetSampleOrdering-EXPERIMENTAL 2020-07-14T13:26:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223831-ReadPosRankSumTest 2020-07-14T13:22:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223851-BaseQuality 2020-07-14T13:22:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223871-SeqIsStoredReadFilter 2020-07-14T13:22:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223891-VariantRecalibrator 2020-07-14T13:26:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223911-PathSeqFilterSpark 2020-07-14T13:26:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223931-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-07-14T13:26:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223951-PlotDenoisedCopyRatios 2020-07-14T13:22:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223971-SplitIntervals 2020-07-14T13:26:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360046223991-UnmarkDuplicates 2020-07-14T13:26:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224011-EvaluateInfoFieldConcordance-BETA 2020-07-14T13:26:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224031-DepthOfCoverage-BETA 2020-07-14T13:26:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224051-PileupSpark-BETA 2020-07-14T13:26:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224071-SplitVcfs-Picard 2020-07-14T13:26:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224091-FilterFuncotations-EXPERIMENTAL 2020-07-14T13:26:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224111-SplitSamByLibrary-Picard 2020-07-14T13:26:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224131-CNNVariantTrain-EXPERIMENTAL 2020-07-14T13:26:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224151-GenotypeGVCFs 2021-01-29T12:01:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224171-TandemRepeat 2020-07-14T13:23:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224191-AnalyzeSaturationMutagenesis-BETA 2020-07-14T13:26:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224211-AS-BaseQualityRankSumTest 2020-07-14T13:23:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224231-FragmentLengthReadFilter 2020-07-14T13:23:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224251-CollectRrbsMetrics-Picard 2020-07-14T13:23:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224271-NotSecondaryAlignmentReadFilter 2020-07-14T13:23:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224291-ValidAlignmentEndReadFilter 2020-07-14T13:26:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224311-QualityScoreDistributionSpark-BETA 2020-07-14T13:26:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224331-DepthPerSampleHC 2020-07-14T13:23:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224351-ReadAnonymizer-EXPERIMENTAL 2020-07-14T13:26:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224371-MappingQualityAvailableReadFilter 2020-07-14T13:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224391-CollectOxoGMetrics-Picard 2020-07-14T13:23:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224411-CreateReadCountPanelOfNormals 2020-07-14T13:23:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224431-CollectDuplicateMetrics-Picard 2020-07-14T13:23:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224451-CountBasesSpark 2020-07-14T13:27:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224471-PrintReadsSpark 2020-07-14T13:27:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224491-CreateSomaticPanelOfNormals-BETA 2020-07-14T13:27:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224511-CheckPileup 2020-07-14T13:27:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224531-GtcToVcf-Picard 2020-07-14T13:23:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224551-ReadLengthReadFilter 2020-07-14T13:23:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360046224571-CleanSam-Picard 2020-07-14T13:23:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786312-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2020-08-03T03:03:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786332-MeanQualityByCycle-Picard 2020-08-03T03:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786352-CollectHiSeqXPfFailMetrics-Picard 2020-08-03T02:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786372-BwaMemIndexImageCreator 2020-08-03T03:03:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786392-WellformedReadFilter 2020-08-03T03:03:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786412-SampleReadFilter 2020-08-03T02:58:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786432-Funcotator 2020-08-03T03:03:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786452-AS-StrandOddsRatio 2020-08-03T02:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786472-FilterVcf-Picard 2020-08-03T02:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786492-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-08-03T03:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786512-AnnotatePairOrientation-EXPERIMENTAL 2020-08-03T03:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786532-VariantEval-BETA 2020-08-03T02:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786552-GnarlyGenotyper-BETA 2020-08-03T03:03:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786572-EstimateLibraryComplexity-Picard 2020-08-03T02:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786592-PrintReadsHeader 2020-08-03T03:03:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786612-ViewSam-Picard 2020-08-03T03:03:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786632-AnnotateVcfWithExpectedAlleleFraction 2020-08-03T03:03:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786652-AllowAllReadsReadFilter 2020-08-03T02:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786672-NotDuplicateReadFilter 2020-08-03T02:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786692-VariantAnnotator 2020-08-03T03:03:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786712-FilterSamReads-Picard 2020-08-03T03:03:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786732-MergePedIntoVcf-Picard 2020-08-03T02:59:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786752-CollectMultipleMetricsSpark-BETA 2020-08-03T03:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786772-CountBases 2020-08-03T03:03:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786792-StrandOddsRatio 2020-08-03T02:59:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786812-HasReadGroupReadFilter 2020-08-03T02:59:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786832-DetermineGermlineContigPloidy 2020-08-03T02:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786852-FindBreakpointEvidenceSpark-BETA 2020-08-03T03:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786872-MappingQuality 2020-08-03T02:59:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786892-VariantsToTable 2020-08-03T03:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786912-CountVariantsSpark 2020-08-03T02:59:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786932-UpdateVCFSequenceDictionary 2020-08-03T03:04:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786952-IlluminaBasecallsToFastq-Picard 2020-08-03T02:59:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786972-FisherStrand 2020-08-03T02:59:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046786992-GetSampleName 2020-08-03T03:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787012-FuncotateSegments-BETA 2020-08-03T03:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787032-GatherBamFiles-Picard 2020-08-03T02:59:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787052-PathSeqBuildReferenceTaxonomy 2020-08-03T02:59:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787072-AS-FisherStrand 2020-08-03T02:59:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787092-GatherVcfs-Picard 2020-08-03T02:59:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787112-MarkDuplicatesWithMateCigar-Picard 2020-08-03T03:04:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787132-AlleleFrequency 2020-08-03T02:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787152-GatherBQSRReports 2020-08-03T02:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787172-MakeSitesOnlyVcf-Picard 2020-08-03T03:04:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787192-IntervalListTools-Picard 2020-08-03T03:04:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787212-CollectInsertSizeMetrics-Picard 2020-08-03T02:59:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787232-CollectReadCounts 2020-08-03T03:04:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787252-FilterIntervals 2020-08-03T03:00:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787272-MappingQualityNotZeroReadFilter 2020-08-03T03:00:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787292-HaplotypeCallerSpark-BETA 2020-08-03T03:04:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787312-CollectJumpingLibraryMetrics-Picard 2020-08-03T03:00:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787332-MateDifferentStrandReadFilter 2020-08-03T03:04:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787352-NonNFastaSize-Picard 2020-08-03T03:04:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787372-BaseRecalibratorSpark-BETA 2020-08-03T03:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787392-CalculateMixingFractions 2020-08-03T03:04:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787412-AccumulateVariantCallingMetrics-Picard 2020-08-03T03:00:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787432-IlluminaBasecallsToSam-Picard 2020-08-03T03:00:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787452-MappingQualityReadFilter 2020-09-25T20:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787472-CreateHadoopBamSplittingIndex-BETA 2020-08-03T03:00:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787492-PrintReads 2020-08-03T03:04:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787512-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-08-03T03:04:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787532-HaplotypeCaller 2020-08-03T03:04:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787572-CountFalsePositives-BETA 2020-08-03T03:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787592-MateUnmappedAndUnmappedReadFilter 2020-08-03T03:00:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787612-CollectIlluminaLaneMetrics-Picard 2020-08-03T03:00:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787632-CountBasesInReference 2020-08-03T03:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787652-PathSeqBwaSpark 2020-08-03T03:04:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787672-MatchingBasesAndQualsReadFilter 2020-08-03T03:00:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787692-MeanQualityByCycleSpark-BETA 2020-08-03T03:04:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787712-CollectBaseDistributionByCycle-Picard 2020-08-03T03:00:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787732-ReblockGVCF-BETA 2020-08-03T03:05:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787752-FixMisencodedBaseQualityReads 2020-08-03T03:05:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787772-LeftAlignAndTrimVariants 2020-08-03T03:05:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787792-BedToIntervalList-Picard 2020-08-03T03:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787812-RemoveNearbyIndels 2020-08-03T03:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787832-CompareDuplicatesSpark-BETA 2020-08-03T03:05:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787852-CollectRawWgsMetrics-Picard 2020-08-03T03:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787872-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-08-03T03:05:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787892-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-08-03T03:01:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787912-PositionBasedDownsampleSam-Picard 2020-08-03T03:01:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787932-ReorderSam-Picard 2020-08-03T03:01:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787952-PostprocessGermlineCNVCalls 2020-08-03T03:05:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787972-FlagStatSpark 2020-08-03T03:05:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360046787992-CollectWgsMetrics-Picard 2020-08-03T03:01:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788012-AS-ReadPosRankSumTest 2020-08-03T03:01:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788032-FifoBuffer-Picard 2020-08-03T03:01:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788052-ExcessHet 2020-08-03T03:01:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788072-VariantFiltration 2020-08-03T03:05:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788112-LikelihoodRankSumTest 2020-08-03T03:01:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788152-RevertBaseQualityScores 2020-08-03T03:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788172-GatherTranches-BETA 2020-08-03T03:01:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788192-DownsampleSam-Picard 2020-08-03T03:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788212-BQSRPipelineSpark-BETA 2020-08-03T03:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788232-PossibleDeNovo 2020-08-03T03:01:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788252-CollectInsertSizeMetricsSpark-BETA 2020-08-03T03:05:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788272-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-08-03T03:05:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788292-IntervalListToBed-Picard 2020-08-03T03:01:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788312-UpdateVcfSequenceDictionary-Picard 2020-08-03T03:01:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788332-MappingQualityZero 2020-08-03T03:01:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788352-CallCopyRatioSegments 2020-08-03T03:01:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788372-ScatterIntervalsByNs-Picard 2020-08-03T03:05:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788392-PlatformReadFilter 2020-08-03T03:01:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788412-BamIndexStats-Picard 2020-08-03T03:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788432-Mutect2 2021-02-19T07:23:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788452-VcfFormatConverter-Picard 2020-08-03T03:05:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788472-PlotModeledSegments 2020-08-03T03:01:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788492-AddOATag-Picard 2020-08-03T03:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788512-MateOnSameContigOrNoMappedMateReadFilter 2020-08-03T03:05:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788532-ApplyBQSRSpark-BETA 2020-08-03T03:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788552-CalculateGenotypePosteriors 2020-08-03T03:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788572-MergeVcfs-Picard 2020-08-03T03:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788592-CollectMultipleMetrics-Picard 2020-08-03T03:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788612-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-08-03T03:01:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788632-QualityScoreDistribution-Picard 2020-08-03T03:02:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788652-FlagStat 2020-08-03T03:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788672-CombineGenotypingArrayVcfs-Picard 2020-08-03T03:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788692-BaitDesigner-Picard 2020-08-03T03:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788712-InbreedingCoeff 2020-08-03T03:02:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788732-FixMateInformation-Picard 2020-08-03T03:02:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788752-ValidateSamFile-Picard 2020-08-03T03:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788772-FastqToSam-Picard 2020-08-03T03:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788792-SortSam-Picard 2020-08-03T03:06:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788812-FuncotatorDataSourceDownloader 2020-08-03T03:02:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788832-MergeSamFiles-Picard 2020-08-03T03:06:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788852-GatherVcfsCloud-BETA 2020-08-03T03:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788872-AnnotateIntervals 2020-08-03T03:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788892-PathSeqScoreSpark 2020-08-03T03:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788912-SplitReads 2020-08-03T03:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788932-AS-MappingQualityRankSumTest 2020-08-03T03:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788952-ReadPosRankSumTest 2020-08-03T03:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788972-SeqIsStoredReadFilter 2020-08-03T03:02:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360046788992-NonZeroReferenceLengthAlignmentReadFilter 2020-08-03T03:02:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789032-VariantRecalibrator 2021-05-03T04:30:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789052-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-08-03T03:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789072-PlotDenoisedCopyRatios 2020-08-03T03:02:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789092-SplitIntervals 2020-08-03T03:06:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789112-StructuralVariationDiscoveryPipelineSpark-BETA 2020-08-03T03:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789132-NonZeroFragmentLengthReadFilter 2020-08-03T03:02:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789152-DepthOfCoverage-BETA 2021-01-26T20:50:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789172-ProperlyPairedReadFilter 2020-08-03T03:02:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789192-CigarContainsNoNOperator 2020-08-03T03:02:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789212-FilterFuncotations-EXPERIMENTAL 2020-08-03T03:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789232-AnalyzeSaturationMutagenesis-BETA 2020-08-03T03:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789252-AS-QualByDepth 2020-08-03T03:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789272-AS-BaseQualityRankSumTest 2020-08-03T03:02:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789292-Concordance 2020-08-03T03:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789312-FragmentLengthReadFilter 2020-08-03T03:02:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789332-FastaReferenceMaker 2020-08-03T03:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789352-QualityScoreDistributionSpark-BETA 2020-08-03T03:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789372-DepthPerSampleHC 2020-08-03T03:03:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789392-RenameSampleInVcf-Picard 2020-08-03T03:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789412-MappingQualityAvailableReadFilter 2021-05-10T12:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789432-ASEReadCounter 2020-08-03T03:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789452-GtcToVcf-Picard 2020-08-03T03:03:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360046789472-CheckTerminatorBlock-Picard 2020-08-03T03:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360046877112-GATK-on-local-HPC-infrastructure 2024-06-25T07:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215611-ChromosomeCounts 2020-08-03T02:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215631-LibraryReadFilter 2020-08-03T02:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215651-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2020-08-03T02:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215671-NonChimericOriginalAlignmentReadFilter 2020-08-03T02:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215691-GenotypeConcordance-Picard 2020-08-03T03:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215711-Pileup 2020-08-03T03:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215731-OverclippedReadFilter 2020-08-03T02:58:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215771-NotProperlyPairedReadFilter 2020-08-03T02:58:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215811-AnalyzeCovariates 2020-08-03T03:03:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215831-RMSMappingQuality 2020-08-03T02:58:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215851-FirstOfPairReadFilter 2020-08-03T02:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215871-CollectQualityYieldMetrics-Picard 2020-08-03T02:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215891-PathSeqPipelineSpark 2020-08-03T03:03:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215911-CalcMetadataSpark-BETA 2020-08-03T03:03:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215931-SecondOfPairReadFilter 2020-08-03T02:58:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215951-AlignmentAgreesWithHeaderReadFilter 2020-08-03T02:58:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215971-CountReads 2020-08-03T03:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360047215991-FixVcfHeader-Picard 2020-08-03T03:03:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216011-CollectHsMetrics-Picard 2020-08-03T03:03:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216031-CountVariants 2020-08-03T03:03:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216051-LiftOverIntervalList-Picard 2020-08-03T02:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216071-BamToBfq-Picard 2020-08-03T02:59:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216091-PrimaryLineReadFilter 2020-08-03T02:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216111--Tool-Documentation-Index 2020-09-18T18:09:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216131-CheckFingerprint-Picard 2020-08-03T02:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216151-UniqueAltReadCount 2020-08-03T02:59:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216171-QualByDepth 2020-08-03T02:59:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216191-NormalizeFasta-Picard 2020-08-03T03:04:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216211-AS-RMSMappingQuality 2020-08-03T02:59:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216231-CNNVariantWriteTensors-EXPERIMENTAL 2020-08-03T03:04:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216251-SamFormatConverter-Picard 2020-08-03T02:59:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216271-ClusterCrosscheckMetrics-Picard 2020-08-03T02:59:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216291-ClipReads 2020-08-03T03:04:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216311-CollectSamErrorMetrics-Picard 2020-08-03T02:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216331-SoftClippedReadFilter 2020-08-03T02:59:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216351-MarkDuplicatesSpark 2020-08-03T03:04:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216371-DepthPerAlleleBySample 2020-08-03T02:59:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216391-CalculateReadGroupChecksum-Picard 2020-08-03T03:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216411-SetNmMdAndUqTags-Picard 2020-08-03T03:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216431-CompareMetrics-Picard 2020-08-03T03:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216451-CalculateFingerprintMetrics-Picard 2020-08-03T02:59:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216471-CompareBaseQualities 2020-08-03T02:59:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216511-BwaSpark-BETA 2020-08-03T03:04:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216531-CollectAlignmentSummaryMetrics-Picard 2020-08-03T02:59:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216571-AnnotateVcfWithBamDepth 2020-08-03T03:04:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216591-CollectSequencingArtifactMetrics-Picard 2020-08-03T02:59:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216611-MappedReadFilter 2020-08-03T02:59:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216631-ExtractSequences-Picard 2020-08-03T03:04:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216651-CalculateContamination 2020-08-03T03:04:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216671-ApplyBQSR 2020-08-03T03:04:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216691-CpxVariantReInterpreterSpark-BETA 2020-08-03T03:04:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216711-PathSeqBuildKmers 2020-08-03T03:04:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216731-StrandBiasBySample 2020-08-03T02:59:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216751-SortSamSpark-BETA 2020-08-03T03:04:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216771-LeftAlignIndels 2020-08-03T03:04:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216791-MappingQualityRankSumTest 2020-08-03T03:00:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216811-SplitSamByNumberOfReads-Picard 2020-08-03T03:04:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216831-FilterMutectCalls 2020-08-03T03:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216851-SelectVariants 2020-08-03T03:04:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216871-ReadGroupReadFilter 2020-08-03T03:00:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216891-GenomicsDBImport 2020-08-03T03:04:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216911-CollectQualityYieldMetricsSpark-BETA 2020-08-03T03:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216931-PlatformUnitReadFilter 2020-08-03T03:00:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216951-MateDistantReadFilter 2020-08-03T03:04:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360047216991-ValidAlignmentStartReadFilter 2020-08-03T03:04:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217011-ReadsPipelineSpark-BETA 2020-08-03T03:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217031-ReplaceSamHeader-Picard 2020-08-03T03:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217051-VcfToIntervalList-Picard 2020-08-03T03:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217071-SetNmAndUqTags-Picard 2020-08-03T03:04:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217091-MarkIlluminaAdapters-Picard 2020-08-03T03:04:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217111-SampleList 2020-08-03T03:00:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217131-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-08-03T03:04:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217151-FragmentLength 2020-08-03T03:00:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217171-CheckIlluminaDirectory-Picard 2020-08-03T03:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217191-CollectTargetedPcrMetrics-Picard 2020-08-03T03:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217211-MergeBamAlignment-Picard 2020-08-03T03:00:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217231-ModelSegments 2020-08-03T03:00:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217251-RevertSamSpark-BETA 2020-08-03T03:05:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217271-ExtractIlluminaBarcodes-Picard 2020-08-03T03:00:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217291-AmbiguousBaseReadFilter 2020-08-03T03:00:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217311-FilterByOrientationBias-EXPERIMENTAL 2020-08-03T03:05:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217331-OriginalAlignment 2020-08-03T03:00:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217351-MarkDuplicates-Picard 2020-08-03T03:00:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217371-CreateSequenceDictionary-Picard 2020-08-03T03:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217391-VcfToAdpc-Picard 2020-08-03T03:00:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217411-GoodCigarReadFilter 2020-08-03T03:01:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217431-NotSupplementaryAlignmentReadFilter 2020-08-03T03:01:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217451-GenotypeSummaries 2020-08-03T03:01:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217471-FilterAlignmentArtifacts-EXPERIMENTAL 2020-08-03T03:05:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217491-PairedReadFilter 2020-08-03T03:01:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217511-GetPileupSummaries 2020-08-03T03:05:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217531-BaseRecalibrator 2020-08-03T03:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217551-ClippingRankSumTest 2020-08-03T03:01:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217571-CompareSAMs-Picard 2020-08-03T03:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217591-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-08-03T03:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217611-DenoiseReadCounts 2020-08-03T03:01:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217631-BaseQualityRankSumTest 2020-08-03T03:01:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217651-ApplyVQSR 2020-08-03T03:05:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217671-GermlineCNVCaller 2020-08-03T03:01:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217691-ReadNameReadFilter 2020-08-03T03:01:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217711-AS-InbreedingCoeff 2020-08-03T03:01:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217731-CollectArraysVariantCallingMetrics-Picard 2020-08-03T03:05:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217751-AddOrReplaceReadGroups-Picard 2020-08-03T03:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217771-CollectVariantCallingMetrics-Picard 2020-08-03T03:01:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217791-CombineGVCFs 2020-08-03T03:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217811-CollectGcBiasMetrics-Picard 2020-08-03T03:01:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217831-LiftoverVcf-Picard 2020-08-03T03:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217851-ReadPosition 2020-08-03T03:01:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217871-Coverage 2020-08-03T03:01:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217891-ReadStrandFilter 2020-08-03T03:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217911-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-08-03T03:01:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217931-ValidateVariants 2020-08-03T03:05:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217951-ExtractSVEvidenceSpark-BETA 2020-08-03T03:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217971-CollectAllelicCounts 2020-08-03T03:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360047217991-CNNScoreVariants 2020-08-03T03:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218011-MethylationTypeCaller-EXPERIMENTAL 2020-08-03T03:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218031-PreprocessIntervals 2020-08-03T03:06:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218051-ReadLengthEqualsCigarLengthReadFilter 2020-08-03T03:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218071-SortVcf-Picard 2020-08-03T03:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218091-PrintVariantsSpark 2020-08-03T03:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218111-ReadGroupBlackListReadFilter 2020-08-03T03:02:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218131-SamToFastq-Picard 2020-08-03T03:06:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218151-CollectIlluminaBasecallingMetrics-Picard 2020-08-03T03:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218171-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-08-03T03:02:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218191-CollectRnaSeqMetrics-Picard 2020-08-03T03:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218211-RevertSam-Picard 2020-08-03T03:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218231-PassesVendorQualityCheckReadFilter 2020-08-03T03:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218251-FixCallSetSampleOrdering-EXPERIMENTAL 2020-08-03T03:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218291-BaseQuality 2020-08-03T03:02:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218311-IntervalOverlapReadFilter 2020-08-03T03:02:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218331-CollectBaseDistributionByCycleSpark-BETA 2020-08-03T03:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218351-PathSeqFilterSpark 2020-08-03T03:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218371-FastaAlternateReferenceMaker 2020-08-03T03:06:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218391-UnmarkDuplicates 2020-08-03T03:06:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218411-EvaluateInfoFieldConcordance-BETA 2020-08-03T03:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218431-SplitNCigarReads 2020-08-03T03:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218451-PileupSpark-BETA 2020-08-03T03:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218471-SplitVcfs-Picard 2020-08-03T03:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218491-SplitSamByLibrary-Picard 2020-08-03T03:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218511-CrosscheckFingerprints-Picard 2020-08-03T03:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218531-CNNVariantTrain-EXPERIMENTAL 2020-08-03T03:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218551-GenotypeGVCFs 2020-08-03T03:06:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218571-TandemRepeat 2020-08-03T03:02:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218591-FindBadGenomicKmersSpark-BETA 2020-08-03T03:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218611-AddCommentsToBam-Picard 2020-08-03T03:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218631-BuildBamIndex-Picard 2020-08-03T03:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218651-CollectRrbsMetrics-Picard 2020-08-03T03:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218671-NotSecondaryAlignmentReadFilter 2020-08-03T03:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218691-FindMendelianViolations-Picard 2020-08-03T03:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218711-ReferenceBases 2020-08-03T03:02:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218731-IndexFeatureFile 2020-08-03T03:03:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218751-MetricsReadFilter 2020-08-03T03:03:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218771-ValidAlignmentEndReadFilter 2020-08-03T03:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218791-AlleleFraction 2020-08-03T03:03:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218811-ConvertSequencingArtifactToOxoG-Picard 2020-08-03T03:03:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218831-OrientationBiasReadCounts 2020-08-03T03:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218851-CountNs 2020-08-03T03:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218871-ReadAnonymizer-EXPERIMENTAL 2020-08-03T03:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218891-CollectOxoGMetrics-Picard 2020-08-03T03:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218911-CreateReadCountPanelOfNormals 2020-08-03T03:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218931-CollectDuplicateMetrics-Picard 2020-08-03T03:03:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218951-CountReadsSpark 2020-08-03T03:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218971-CountBasesSpark 2020-08-03T03:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360047218991-PrintReadsSpark 2020-08-03T03:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360047219011-FilterVariantTranches 2020-08-03T03:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360047219031-CreateSomaticPanelOfNormals-BETA 2020-09-20T05:51:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360047219051-CheckPileup 2020-08-03T03:07:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360047219071-ReadLengthReadFilter 2020-08-03T03:03:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360047219091-CleanSam-Picard 2020-08-03T03:03:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360047232772--Notebook-Intro-to-using-Mutect2-for-somatic-data 2024-06-25T07:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360047717551-Downsampling-in-GATK 2020-09-03T18:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360049493892-DRAGEN-GATK-update-Upcoming-webinar-and-pipeline-release-timeframe 2024-07-01T17:20:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360050354712-What-is-physical-phasing 2024-07-22T20:32:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360050722212-FAQ-for-Mutect2 2024-07-08T19:43:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813352-ChromosomeCounts 2020-10-20T19:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813372-NonChimericOriginalAlignmentReadFilter 2020-10-20T19:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813392-GenotypeConcordance-Picard 2020-10-20T20:03:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813412-OverclippedReadFilter 2020-10-20T19:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813432-NotProperlyPairedReadFilter 2020-10-20T19:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813472-CollectQualityYieldMetrics-Picard 2020-10-20T19:58:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813492-CalcMetadataSpark-BETA 2020-10-20T20:04:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813512-SecondOfPairReadFilter 2020-10-20T19:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813532-AlignmentAgreesWithHeaderReadFilter 2020-10-20T19:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813552-FilterVcf-Picard 2020-10-20T19:58:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813572-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2020-10-20T20:04:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813592-FixVcfHeader-Picard 2020-10-20T20:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813612-GnarlyGenotyper-BETA 2020-10-20T20:04:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813632-EstimateLibraryComplexity-Picard 2020-10-20T19:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813652-AnnotateVcfWithExpectedAlleleFraction 2020-10-20T20:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813672-CountVariants 2020-10-20T20:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813692-AllowAllReadsReadFilter 2020-10-20T19:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813712-LiftOverIntervalList-Picard 2020-10-20T19:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813752-BamToBfq-Picard 2020-10-20T19:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813772-VariantAnnotator 2020-10-20T20:04:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813792-FilterSamReads-Picard 2020-10-20T20:04:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813812-PrimaryLineReadFilter 2020-10-20T19:59:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813832-CollectMultipleMetricsSpark-BETA 2020-10-20T20:04:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813852-StrandOddsRatio 2020-10-20T19:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813872--Tool-Documentation-Index 2020-10-20T20:04:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813892-FindBreakpointEvidenceSpark-BETA 2020-10-20T20:04:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813912-MappingQuality 2020-10-20T19:59:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813952-NormalizeFasta-Picard 2020-10-20T20:04:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360050813972-UpdateVCFSequenceDictionary 2020-10-20T20:04:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814012-IlluminaBasecallsToFastq-Picard 2020-10-20T19:59:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814032-FisherStrand 2020-10-20T19:59:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814052-ClusterCrosscheckMetrics-Picard 2020-10-20T19:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814072-SoftClippedReadFilter 2020-10-20T19:59:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814092-GetSampleName 2020-10-20T20:04:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814112-MarkDuplicatesSpark 2020-10-20T20:04:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814152-CalculateFingerprintMetrics-Picard 2020-10-20T19:59:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814172-AS-FisherStrand 2020-10-20T19:59:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814192-CollectAlignmentSummaryMetrics-Picard 2020-10-20T19:59:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814212-CollectSequencingArtifactMetrics-Picard 2020-10-20T19:59:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814232-GatherVcfs-Picard 2020-10-20T19:59:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814252-MappedReadFilter 2020-10-20T19:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814272-ExtractSequences-Picard 2020-10-20T20:04:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814292-CalculateContamination 2020-10-20T20:04:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814312-ApplyBQSR 2020-10-20T20:04:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814352-StrandBiasBySample 2020-10-20T20:00:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814392-SortSamSpark-BETA 2020-10-20T20:04:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814412-FilterIntervals 2020-10-20T20:00:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814432-MappingQualityRankSumTest 2020-10-20T20:00:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814452-HaplotypeCallerSpark-BETA 2020-10-20T20:04:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814472-SplitSamByNumberOfReads-Picard 2020-10-20T20:04:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814492-MateDifferentStrandReadFilter 2020-10-20T20:04:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814512-NonNFastaSize-Picard 2020-10-20T20:04:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814532-ReadGroupReadFilter 2020-10-20T20:00:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814552-MappingQualityReadFilter 2020-10-20T20:05:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814572-PlatformUnitReadFilter 2020-10-20T20:00:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814592-CreateHadoopBamSplittingIndex-BETA 2020-10-20T20:00:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814612-HaplotypeCaller 2021-02-20T21:51:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814632-ReadsPipelineSpark-BETA 2020-10-20T20:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814652-ReplaceSamHeader-Picard 2020-10-20T20:05:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814672-CountFalsePositives-BETA 2020-10-20T20:05:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814712-CollectIlluminaLaneMetrics-Picard 2020-10-20T20:00:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814732-CountBasesInReference 2020-10-20T20:05:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814752-VcfToIntervalList-Picard 2020-10-20T20:05:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814792-CollectTargetedPcrMetrics-Picard 2020-10-20T20:05:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814812-FixMisencodedBaseQualityReads 2020-10-20T20:05:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814832-RevertSamSpark-BETA 2020-10-20T20:05:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814852-CollectRawWgsMetrics-Picard 2020-10-20T20:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814872-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2020-10-20T20:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814892-VcfToAdpc-Picard 2020-10-20T20:01:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814912-PostprocessGermlineCNVCalls 2020-10-20T20:05:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814932-NotSupplementaryAlignmentReadFilter 2020-10-20T20:01:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814952-FlagStatSpark 2020-10-20T20:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814972-FilterAlignmentArtifacts-EXPERIMENTAL 2020-10-20T20:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360050814992-CollectWgsMetrics-Picard 2020-10-20T20:01:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815012-AS-ReadPosRankSumTest 2020-10-20T20:01:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815032-VariantFiltration 2020-10-20T20:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815052-LikelihoodRankSumTest 2020-10-20T20:01:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815072-BaseRecalibrator 2021-10-08T07:43:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815092-RevertBaseQualityScores 2020-10-20T20:05:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815112-GatherTranches-BETA 2020-10-20T20:01:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815132-ClippingRankSumTest 2020-10-20T20:01:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815152-BQSRPipelineSpark-BETA 2020-10-20T20:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815172-BaseQualityRankSumTest 2020-10-20T20:01:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815192-IntervalListToBed-Picard 2020-10-20T20:01:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815212-ReadNameReadFilter 2020-10-20T20:01:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815232-MappingQualityZero 2020-10-20T20:01:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815252-ScatterIntervalsByNs-Picard 2020-10-20T20:05:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815272-AS-InbreedingCoeff 2020-10-20T20:01:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815292-PlatformReadFilter 2020-10-20T20:01:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815312-CollectArraysVariantCallingMetrics-Picard 2021-09-24T18:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815332-VcfFormatConverter-Picard 2020-10-20T20:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815352-CollectVariantCallingMetrics-Picard 2020-10-20T20:01:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815372-CombineGVCFs 2020-10-20T20:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815392-LiftoverVcf-Picard 2020-10-20T20:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815412-AddOATag-Picard 2020-10-20T20:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815432-MateOnSameContigOrNoMappedMateReadFilter 2020-10-20T20:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815452-Coverage 2020-10-20T20:02:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815472-MergeVcfs-Picard 2020-10-20T20:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815492-ValidateVariants 2020-10-20T20:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815512-ExtractSVEvidenceSpark-BETA 2020-10-20T20:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815532-CollectAllelicCounts 2020-10-20T20:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815552-CNNScoreVariants 2020-10-20T20:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815572-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2020-10-20T20:02:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815592-MethylationTypeCaller-EXPERIMENTAL 2020-10-20T20:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815612-PreprocessIntervals 2020-10-20T20:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815632-QualityScoreDistribution-Picard 2020-10-20T20:02:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815652-CombineGenotypingArrayVcfs-Picard 2020-10-20T20:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815672-BaitDesigner-Picard 2020-10-20T20:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815692-InbreedingCoeff 2020-10-20T20:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815712-ReadLengthEqualsCigarLengthReadFilter 2020-10-20T20:06:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815732-SortVcf-Picard 2020-10-20T20:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815752-FastqToSam-Picard 2020-10-20T20:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815772-ReadGroupBlackListReadFilter 2020-10-20T20:02:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815792-FuncotatorDataSourceDownloader 2020-10-20T20:02:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815812-ConvertHeaderlessHadoopBamShardToBam-BETA 2020-10-20T20:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815832-CollectRnaSeqMetrics-Picard 2020-10-20T20:02:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815852-SplitReads 2020-10-20T20:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815872-VariantRecalibrator 2020-10-20T20:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815892-PlotDenoisedCopyRatios 2020-10-20T20:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815912-FastaAlternateReferenceMaker 2020-10-20T20:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815932-UnmarkDuplicates 2020-10-20T20:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815952-EvaluateInfoFieldConcordance-BETA 2020-10-20T20:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815972-SplitNCigarReads 2020-10-20T20:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360050815992-NonZeroFragmentLengthReadFilter 2020-10-20T20:03:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816012-PileupSpark-BETA 2020-10-20T20:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816032-CigarContainsNoNOperator 2020-10-20T20:03:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816052-CrosscheckFingerprints-Picard 2020-10-20T20:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816072-GenotypeGVCFs 2020-10-20T20:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816092-AddCommentsToBam-Picard 2020-10-20T20:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816112-AS-QualByDepth 2020-10-20T20:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816132-BuildBamIndex-Picard 2020-10-20T20:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816152-NotSecondaryAlignmentReadFilter 2020-10-20T20:03:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816172-FastaReferenceMaker 2020-10-20T20:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816192-ConvertSequencingArtifactToOxoG-Picard 2020-10-20T20:03:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816212-OrientationBiasReadCounts 2020-10-20T20:03:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816232-CountNs 2020-10-20T20:03:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816252-RenameSampleInVcf-Picard 2020-10-20T20:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816272-ReadAnonymizer-EXPERIMENTAL 2020-10-20T20:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816292-CollectOxoGMetrics-Picard 2020-10-20T20:03:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816312-CreateSomaticPanelOfNormals-BETA 2020-10-20T20:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360050816332-CheckPileup 2020-10-20T20:07:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304151-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2020-10-20T20:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304171-LibraryReadFilter 2020-10-20T19:58:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304191-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2020-10-20T19:58:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304211-MeanQualityByCycle-Picard 2020-10-20T20:03:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304231-CollectHiSeqXPfFailMetrics-Picard 2020-10-20T19:58:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304251-Pileup 2020-10-20T20:03:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304291-BwaMemIndexImageCreator 2020-10-20T20:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304311-WellformedReadFilter 2020-10-20T20:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304331-SampleReadFilter 2020-10-20T19:58:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304351-AnalyzeCovariates 2020-10-20T20:03:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304371-RMSMappingQuality 2020-10-20T19:58:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304391-FirstOfPairReadFilter 2020-10-20T19:58:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304411-Funcotator 2020-10-20T20:04:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304431-PathSeqPipelineSpark 2020-10-20T20:04:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304451-AS-StrandOddsRatio 2020-10-20T19:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304471-AnnotatePairOrientation-EXPERIMENTAL 2020-10-20T20:04:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304491-VariantEval-BETA 2020-10-20T19:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304511-CountReads 2020-10-20T20:04:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304551-CollectHsMetrics-Picard 2020-10-20T20:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304571-PrintReadsHeader 2020-10-20T20:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304591-ViewSam-Picard 2020-10-20T20:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304611-NotDuplicateReadFilter 2020-10-20T19:59:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304631-MergePedIntoVcf-Picard 2020-10-20T19:59:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304651-CountBases 2020-10-20T20:04:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304671-CheckFingerprint-Picard 2020-10-20T19:59:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304691-HasReadGroupReadFilter 2020-10-20T19:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304711-DetermineGermlineContigPloidy 2021-11-17T09:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304731-UniqueAltReadCount 2020-10-20T19:59:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304751-QualByDepth 2020-10-20T19:59:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304771-VariantsToTable 2020-10-20T20:04:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304791-AS-RMSMappingQuality 2020-10-20T19:59:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304811-CNNVariantWriteTensors-EXPERIMENTAL 2020-10-20T20:04:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304831-CountVariantsSpark 2020-10-20T19:59:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304851-SamFormatConverter-Picard 2020-10-20T19:59:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304891-GeneExpressionEvaluation-BETA 2023-11-07T19:48:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304911-ClipReads 2020-10-20T20:04:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304931-CollectSamErrorMetrics-Picard 2020-10-20T19:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304951-DepthPerAlleleBySample 2020-10-20T19:59:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304971-CalculateReadGroupChecksum-Picard 2020-10-20T20:04:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360051304991-SetNmMdAndUqTags-Picard 2020-10-20T20:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305011-CompareMetrics-Picard 2020-10-20T20:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305031-FuncotateSegments-BETA 2020-10-20T20:04:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305051-GatherBamFiles-Picard 2020-10-20T19:59:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305071-PathSeqBuildReferenceTaxonomy 2020-10-20T19:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305111-CompareBaseQualities 2020-10-20T19:59:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305131-BwaSpark-BETA 2020-10-20T20:04:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305151-AnnotateVcfWithBamDepth 2020-10-20T20:04:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305171-MarkDuplicatesWithMateCigar-Picard 2020-10-20T20:04:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305191-AlleleFrequency 2020-10-20T19:59:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305211-GatherBQSRReports 2020-10-20T19:59:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305231-CpxVariantReInterpreterSpark-BETA 2020-10-20T20:04:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305251-PathSeqBuildKmers 2020-10-20T20:04:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305271-MakeSitesOnlyVcf-Picard 2020-10-20T20:04:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305291-IntervalListTools-Picard 2020-10-20T20:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305311-CollectInsertSizeMetrics-Picard 2020-10-20T20:00:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305331-LearnReadOrientationModel 2020-10-20T20:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305351-CollectReadCounts 2020-10-20T20:04:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305371-LeftAlignIndels 2020-10-20T20:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305391-MappingQualityNotZeroReadFilter 2020-10-20T20:00:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305431-CollectJumpingLibraryMetrics-Picard 2020-10-20T20:00:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305471-FilterMutectCalls 2020-10-20T20:04:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305491-BaseRecalibratorSpark-BETA 2020-10-20T20:04:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305511-CalculateMixingFractions 2020-10-20T20:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305531-SelectVariants 2020-10-20T20:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305551-AccumulateVariantCallingMetrics-Picard 2020-10-20T20:00:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305571-IlluminaBasecallsToSam-Picard 2020-10-20T20:00:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305591-GenomicsDBImport 2021-02-01T20:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305611-CollectQualityYieldMetricsSpark-BETA 2020-10-20T20:05:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305631-PrintReads 2020-10-20T20:05:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305651-BwaAndMarkDuplicatesPipelineSpark-BETA 2020-10-20T20:05:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305671-MateDistantReadFilter 2020-10-20T20:05:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305691-ValidAlignmentStartReadFilter 2020-10-20T20:05:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305711-MateUnmappedAndUnmappedReadFilter 2020-10-20T20:00:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305751-SetNmAndUqTags-Picard 2020-10-20T20:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305771-PathSeqBwaSpark 2020-10-20T20:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305791-MarkIlluminaAdapters-Picard 2021-06-15T15:52:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305811-SampleList 2020-10-20T20:00:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305831-MatchingBasesAndQualsReadFilter 2020-10-20T20:00:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305851-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2020-10-20T20:05:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305871-MeanQualityByCycleSpark-BETA 2020-10-20T20:05:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305891-FragmentLength 2020-10-20T20:00:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305911-CheckIlluminaDirectory-Picard 2020-10-20T20:05:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305931-CollectBaseDistributionByCycle-Picard 2020-10-20T20:00:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305951-ReblockGVCF-BETA 2020-10-20T20:05:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305971-MergeBamAlignment-Picard 2020-10-20T20:00:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360051305991-LeftAlignAndTrimVariants 2020-10-20T20:05:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306011-ModelSegments 2020-10-20T20:00:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306031-ExtractIlluminaBarcodes-Picard 2020-10-20T20:00:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306051-AmbiguousBaseReadFilter 2020-10-20T20:00:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306071-BedToIntervalList-Picard 2020-11-23T23:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306091-RemoveNearbyIndels 2020-10-20T20:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306111-CompareDuplicatesSpark-BETA 2020-10-20T20:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306131-FilterByOrientationBias-EXPERIMENTAL 2020-10-20T20:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306151-OriginalAlignment 2020-10-20T20:01:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306171-MarkDuplicates-Picard 2021-03-04T02:47:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306191-CreateSequenceDictionary-Picard 2020-10-20T20:05:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306231-GoodCigarReadFilter 2020-10-20T20:01:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306271-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-10-20T20:01:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306291-PositionBasedDownsampleSam-Picard 2020-10-20T20:01:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306311-ReorderSam-Picard 2020-10-20T20:01:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306331-GenotypeSummaries 2020-10-20T20:01:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306351-PairedReadFilter 2020-10-20T20:01:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306371-GetPileupSummaries 2020-10-20T20:05:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306391-FifoBuffer-Picard 2020-10-20T20:01:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306411-ExcessHet 2020-10-20T20:01:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306431-DownsampleSam-Picard 2020-10-20T20:05:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306451-CompareSAMs-Picard 2020-10-20T20:05:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306471-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2020-10-20T20:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306511-PossibleDeNovo 2020-10-20T20:01:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306531-CollectInsertSizeMetricsSpark-BETA 2020-10-20T20:05:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306551-DenoiseReadCounts 2020-10-20T20:01:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306571-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2020-10-20T20:05:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306591-ApplyVQSR 2020-10-20T20:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306611-GermlineCNVCaller 2020-10-20T20:01:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306631-UpdateVcfSequenceDictionary-Picard 2020-10-20T20:01:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306651-CallCopyRatioSegments 2020-10-20T20:01:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306671-BamIndexStats-Picard 2020-10-20T20:05:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306691-Mutect2 2020-10-20T20:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306711-AddOrReplaceReadGroups-Picard 2020-10-20T20:01:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306731-PlotModeledSegments 2020-10-20T20:01:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306751-CollectGcBiasMetrics-Picard 2020-10-20T20:01:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306771-ReadPosition 2020-10-20T20:01:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306791-ReadStrandFilter 2020-10-20T20:02:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306811-ApplyBQSRSpark-BETA 2020-10-20T20:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306831-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2020-10-20T20:02:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306851-CalculateGenotypePosteriors 2020-10-20T20:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306871-CollectMultipleMetrics-Picard 2020-10-20T20:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306891-FlagStat 2020-10-20T20:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306911-FixMateInformation-Picard 2020-10-20T20:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306931-PrintVariantsSpark 2020-10-20T20:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306951-ValidateSamFile-Picard 2020-10-20T20:02:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306971-BpmToNormalizationManifestCsv-Picard 2020-10-20T20:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360051306991-SamToFastq-Picard 2020-10-20T20:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307011-SortSam-Picard 2020-10-20T20:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307031-CollectIlluminaBasecallingMetrics-Picard 2020-10-20T20:02:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307051-MergeSamFiles-Picard 2020-10-20T20:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307071-GatherVcfsCloud-BETA 2020-10-20T20:02:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307091-AnnotateIntervals 2020-10-20T20:06:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307111-PathSeqScoreSpark 2020-10-20T20:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307151-RevertSam-Picard 2020-10-20T20:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307171-PassesVendorQualityCheckReadFilter 2020-10-20T20:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307231-AS-MappingQualityRankSumTest 2022-12-04T17:14:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307271-FixCallSetSampleOrdering-EXPERIMENTAL 2020-10-20T20:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307291-ReadPosRankSumTest 2020-10-20T20:02:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307311-BaseQuality 2020-10-20T20:02:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307331-SeqIsStoredReadFilter 2020-10-20T20:02:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307351-IntervalOverlapReadFilter 2020-10-20T20:02:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307371-NonZeroReferenceLengthAlignmentReadFilter 2020-10-20T20:02:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307391-CollectBaseDistributionByCycleSpark-BETA 2020-10-20T20:06:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307411-PathSeqFilterSpark 2020-10-20T20:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307431-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2020-10-20T20:06:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307451-SplitIntervals 2020-10-20T20:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307471-StructuralVariationDiscoveryPipelineSpark-BETA 2020-10-20T20:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307491-DepthOfCoverage-BETA 2020-10-20T20:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307511-ProperlyPairedReadFilter 2020-10-20T20:03:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307531-SplitVcfs-Picard 2020-10-20T20:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307551-FilterFuncotations-EXPERIMENTAL 2020-10-20T20:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307571-SplitSamByLibrary-Picard 2020-10-20T20:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307591-CNNVariantTrain-EXPERIMENTAL 2020-10-20T20:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307611-TandemRepeat 2020-10-20T20:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307631-FindBadGenomicKmersSpark-BETA 2020-10-20T20:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307651-AnalyzeSaturationMutagenesis-BETA 2020-10-20T20:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307671-AS-BaseQualityRankSumTest 2020-10-20T20:03:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307691-Concordance 2020-10-20T20:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307711-FragmentLengthReadFilter 2020-10-20T20:03:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307731-CollectRrbsMetrics-Picard 2020-10-20T20:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307751-FindMendelianViolations-Picard 2020-10-20T20:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307771-ReferenceBases 2020-10-20T20:03:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307791-IndexFeatureFile 2020-10-20T20:03:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307811-MetricsReadFilter 2020-10-20T20:03:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307831-ValidAlignmentEndReadFilter 2020-10-20T20:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307851-QualityScoreDistributionSpark-BETA 2020-10-20T20:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307871-DepthPerSampleHC 2020-10-20T20:03:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307891-AlleleFraction 2020-10-20T20:03:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307931-MappingQualityAvailableReadFilter 2020-10-20T20:03:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307951-CreateReadCountPanelOfNormals 2020-10-20T20:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307971-CollectDuplicateMetrics-Picard 2020-10-20T20:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360051307991-CountReadsSpark 2020-10-20T20:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308011-CountBasesSpark 2020-10-20T20:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308031-PrintReadsSpark 2020-10-20T20:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308051-ASEReadCounter 2020-10-20T20:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches 2020-10-20T20:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308191-GtcToVcf-Picard 2020-10-20T20:03:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308211-CheckTerminatorBlock-Picard 2020-10-20T20:03:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308231-ReadLengthReadFilter 2020-10-20T20:03:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360051308251-CleanSam-Picard 2020-10-20T20:03:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360051699511-Mutect2-Webinar-Announcement-and-A-Call-for-Questions-From-Our-Community 2024-07-01T17:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360051705571--GATK-4-1-9-0-release 2024-07-01T17:19:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360052489832-Known-Issue-with-CNNScoreVariants-version-4-1-9-0 2024-06-25T07:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines 2023-10-30T10:35:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360055062832-New-Year-update-GATK-takes-on-2021 2022-04-21T02:23:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360056138571-GenomicsDBImport-usage-and-performance-guidelines 2025-02-19T13:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360056402031-GATK-on-the-cloud-with-Azure 2024-06-25T07:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360056798851--GATK-4-2-release 2024-07-01T17:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967632-LibraryReadFilter 2021-02-22T23:01:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967652-MeanQualityByCycle-Picard 2021-02-22T23:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967672-CollectHiSeqXPfFailMetrics-Picard 2021-02-22T23:01:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967692-GenotypeConcordance-Picard 2021-02-22T23:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967712-Pileup 2021-02-22T23:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967732-OverclippedReadFilter 2021-02-22T23:01:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967752-AnalyzeCovariates 2021-02-22T23:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967772-Funcotator 2021-02-22T23:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967792-CollectQualityYieldMetrics-Picard 2021-02-22T23:02:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967812-CalcMetadataSpark-BETA 2021-02-22T23:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967832-SecondOfPairReadFilter 2021-02-22T23:02:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967852-AS-StrandOddsRatio 2021-02-22T23:02:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967872-FilterVcf-Picard 2021-02-22T23:02:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967892-VariantEval-BETA 2021-02-22T23:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967912-FixVcfHeader-Picard 2021-02-22T23:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967932-CollectHsMetrics-Picard 2021-02-22T23:06:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967952-GnarlyGenotyper-BETA 2021-02-22T23:06:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360056967992-PrintReadsHeader 2021-02-22T23:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968012-ViewSam-Picard 2021-02-22T23:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968032-AnnotateVcfWithExpectedAlleleFraction 2021-02-22T23:06:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968052-CountVariants 2021-02-22T23:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968072-LiftOverIntervalList-Picard 2021-02-22T23:02:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968092-BamToBfq-Picard 2021-02-22T23:02:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968112-VariantAnnotator 2021-02-22T23:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968132-FilterSamReads-Picard 2021-02-22T23:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968152-CollectMultipleMetricsSpark-BETA 2021-02-22T23:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968172-StrandOddsRatio 2021-02-22T23:02:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968212-CheckFingerprint-Picard 2021-02-22T23:02:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968232-DetermineGermlineContigPloidy 2021-02-22T23:02:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968252-MappingQuality 2021-02-22T23:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968272-QualByDepth 2021-02-22T23:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968292-VariantsToTable 2021-02-22T23:06:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968312-CNNVariantWriteTensors-EXPERIMENTAL 2021-02-22T23:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968352-IlluminaBasecallsToFastq-Picard 2021-02-22T23:02:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968372-SamFormatConverter-Picard 2021-02-22T23:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968392-FisherStrand 2021-02-22T23:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968412-GeneExpressionEvaluation-BETA 2021-02-22T23:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968432-ClipReads 2021-02-22T23:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968452-SoftClippedReadFilter 2021-02-22T23:02:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968472-GetSampleName 2021-02-22T23:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968492-CalculateFingerprintMetrics-Picard 2021-02-22T23:02:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968512-CollectAlignmentSummaryMetrics-Picard 2021-02-22T23:02:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968532-CollectSequencingArtifactMetrics-Picard 2021-02-22T23:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968552-GatherVcfs-Picard 2021-02-22T23:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968572-MappedReadFilter 2021-06-30T05:48:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968592-ExtractSequences-Picard 2021-02-22T23:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968612-GatherBQSRReports 2021-02-22T23:03:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968632-CalculateContamination 2021-02-22T23:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968652-ApplyBQSR 2021-02-22T23:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968672-CpxVariantReInterpreterSpark-BETA 2021-02-22T23:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968692-MakeSitesOnlyVcf-Picard 2021-02-22T23:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968712-CollectInsertSizeMetrics-Picard 2021-02-22T23:03:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968732-SortSamSpark-BETA 2021-02-22T23:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968752-LeftAlignIndels 2021-02-22T23:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968772-FilterIntervals 2021-02-22T23:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968792-HaplotypeCallerSpark-BETA 2021-02-22T23:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968812-FilterMutectCalls 2021-02-22T23:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968832-CalculateMixingFractions 2021-02-22T23:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968852-AccumulateVariantCallingMetrics-Picard 2021-02-22T23:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968872-IlluminaBasecallsToSam-Picard 2021-02-22T23:03:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968892-ReadGroupReadFilter 2021-02-22T23:03:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968932-CollectQualityYieldMetricsSpark-BETA 2021-02-22T23:06:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968952-PlatformUnitReadFilter 2021-02-22T23:03:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968972-CreateHadoopBamSplittingIndex-BETA 2021-02-22T23:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360056968992-BwaAndMarkDuplicatesPipelineSpark-BETA 2021-02-22T23:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969012-HaplotypeCaller 2021-11-02T08:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969032-ReplaceSamHeader-Picard 2021-02-22T23:07:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969052-MateUnmappedAndUnmappedReadFilter 2021-02-22T23:03:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969072-CollectIlluminaLaneMetrics-Picard 2021-02-22T23:03:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969092-CountBasesInReference 2021-02-22T23:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969112-SetNmAndUqTags-Picard 2021-02-22T23:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969132-PathSeqBwaSpark 2024-03-16T04:51:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969152-MatchingBasesAndQualsReadFilter 2021-02-22T23:03:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969172-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2021-02-22T23:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969192-CollectBaseDistributionByCycle-Picard 2021-02-22T23:03:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969212-FixMisencodedBaseQualityReads 2021-02-22T23:07:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969232-LeftAlignAndTrimVariants 2021-02-22T23:07:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969252-ExtractIlluminaBarcodes-Picard 2021-02-22T23:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969272-CompareDuplicatesSpark-BETA 2021-02-22T23:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969292-CollectRawWgsMetrics-Picard 2021-02-22T23:07:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969312-GoodCigarReadFilter 2022-06-19T07:32:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969332-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-02-22T23:04:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969352-PositionBasedDownsampleSam-Picard 2021-02-22T23:04:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969372-PostprocessGermlineCNVCalls 2021-02-22T23:07:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969392-GetPileupSummaries 2021-02-22T23:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969412-BaseRecalibrator 2021-02-22T23:07:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969432-GatherTranches-BETA 2021-02-22T23:04:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969452-DownsampleSam-Picard 2021-02-22T23:07:31Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969472-ClippingRankSumTest 2021-02-22T23:04:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969492-BQSRPipelineSpark-BETA 2021-02-22T23:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969512-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-02-22T23:07:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969532-BaseQualityRankSumTest 2024-07-30T15:32:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969552-IntervalListToBed-Picard 2021-02-22T23:04:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969572-ApplyVQSR 2021-02-22T23:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969592-ReadNameReadFilter 2021-02-22T23:04:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969612-MappingQualityZero 2021-02-22T23:04:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969632-CallCopyRatioSegments 2021-02-22T23:04:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969652-PlatformReadFilter 2021-02-22T23:04:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969672-BamIndexStats-Picard 2021-02-22T23:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969692-Mutect2 2023-05-10T14:12:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969712-CollectArraysVariantCallingMetrics-Picard 2021-02-22T23:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969732-PlotModeledSegments 2021-02-22T23:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969752-CollectVariantCallingMetrics-Picard 2021-02-22T23:04:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969772-CombineGVCFs 2021-02-22T23:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969792-LiftoverVcf-Picard 2021-02-22T23:07:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969812-AddOATag-Picard 2021-02-22T23:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969832-MateOnSameContigOrNoMappedMateReadFilter 2021-02-22T23:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969852-MergeVcfs-Picard 2021-11-17T00:42:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969872-ValidateVariants 2021-02-22T23:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969892-ExtractSVEvidenceSpark-BETA 2021-02-22T23:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969912-CollectAllelicCounts 2021-02-22T23:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969932-CNNScoreVariants 2021-02-22T23:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969952-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2021-02-22T23:04:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969972-QualityScoreDistribution-Picard 2021-02-22T23:04:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360056969992-BaitDesigner-Picard 2021-02-22T23:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970012-ReadLengthEqualsCigarLengthReadFilter 2021-02-22T23:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970032-FixMateInformation-Picard 2021-02-22T23:04:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970052-SortVcf-Picard 2021-02-22T23:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970072-PrintVariantsSpark 2021-02-22T23:07:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970092-ReadGroupBlackListReadFilter 2021-02-22T23:05:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970112-SamToFastq-Picard 2021-02-22T23:08:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970132-GatherVcfsCloud-BETA 2021-02-22T23:05:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970152-AnnotateIntervals 2021-02-22T23:08:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970172-SplitReads 2021-02-22T23:08:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970192-ReadPosRankSumTest 2021-02-22T23:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970232-VariantRecalibrator 2021-07-12T03:17:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970252-PathSeqFilterSpark 2021-02-22T23:08:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970272-PlotDenoisedCopyRatios 2021-02-22T23:05:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970292-SplitIntervals 2021-02-22T23:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970312-SplitNCigarReads 2021-02-22T23:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970332-DepthOfCoverage-BETA 2021-02-22T23:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970352-CigarContainsNoNOperator 2021-02-22T23:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970372-SplitVcfs-Picard 2021-02-22T23:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970392-SplitSamByLibrary-Picard 2021-02-22T23:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970432-GenotypeGVCFs 2022-01-14T18:03:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970472-TandemRepeat 2021-02-22T23:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970492-AnalyzeSaturationMutagenesis-BETA 2021-02-22T23:08:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970512-AS-QualByDepth 2021-02-22T23:08:22Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970532-AS-BaseQualityRankSumTest 2021-02-22T23:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970552-FragmentLengthReadFilter 2021-02-22T23:05:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970572-BuildBamIndex-Picard 2021-02-22T23:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970592-NotSecondaryAlignmentReadFilter 2021-02-22T23:05:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970612-MetricsReadFilter 2021-02-22T23:05:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970632-FastaReferenceMaker 2021-02-22T23:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970652-QualityScoreDistributionSpark-BETA 2021-02-22T23:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970672-AlleleFraction 2021-02-22T23:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970692-ConvertSequencingArtifactToOxoG-Picard 2021-02-22T23:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970712-RenameSampleInVcf-Picard 2021-02-22T23:08:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970732-ReadAnonymizer-EXPERIMENTAL 2021-02-22T23:08:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970752-MappingQualityAvailableReadFilter 2021-02-22T23:05:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970772-CountReadsSpark 2021-02-22T23:08:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970812-FilterVariantTranches 2021-02-22T23:08:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360056970832-CleanSam-Picard 2021-02-22T23:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438151-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2021-02-22T23:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438171-ChromosomeCounts 2021-02-22T23:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438191-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2021-02-22T23:01:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438211-NonChimericOriginalAlignmentReadFilter 2021-02-22T23:01:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438231-BwaMemIndexImageCreator 2021-02-22T23:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438251-NotProperlyPairedReadFilter 2021-06-01T08:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438291-WellformedReadFilter 2021-06-30T05:46:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438311-SampleReadFilter 2021-02-22T23:01:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438331-RMSMappingQuality 2021-02-22T23:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438351-FirstOfPairReadFilter 2021-02-22T23:02:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438371-PathSeqPipelineSpark 2021-02-22T23:06:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438391-AlignmentAgreesWithHeaderReadFilter 2021-02-22T23:02:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438411-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2021-02-22T23:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438431-CountReads 2021-02-22T23:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438451-EstimateLibraryComplexity-Picard 2021-02-22T23:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438471-AllowAllReadsReadFilter 2021-02-22T23:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438491-NotDuplicateReadFilter 2021-02-22T23:02:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438511-MergePedIntoVcf-Picard 2021-02-22T23:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438531-PrimaryLineReadFilter 2021-02-22T23:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438551-CountBases 2021-02-22T23:06:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438571--Tool-Documentation-Index 2025-05-25T21:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438591-HasReadGroupReadFilter 2021-02-22T23:02:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438611-FindBreakpointEvidenceSpark-BETA 2021-02-22T23:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438631-UniqueAltReadCount 2021-02-22T23:02:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438651-NormalizeFasta-Picard 2021-02-22T23:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438671-AS-RMSMappingQuality 2021-02-22T23:02:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438691-CountVariantsSpark 2021-02-22T23:02:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438711-UpdateVCFSequenceDictionary 2021-02-22T23:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438731-ClusterCrosscheckMetrics-Picard 2021-02-22T23:02:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438751-CollectSamErrorMetrics-Picard 2021-02-22T23:02:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438771-MarkDuplicatesSpark 2021-09-03T07:11:58Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438791-DepthPerAlleleBySample 2021-02-22T23:02:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438811-CalculateReadGroupChecksum-Picard 2021-02-22T23:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438831-SetNmMdAndUqTags-Picard 2021-02-22T23:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438851-CompareMetrics-Picard 2021-02-22T23:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438871-FuncotateSegments-BETA 2021-02-22T23:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438891-GatherBamFiles-Picard 2021-02-22T23:02:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438911-PathSeqBuildReferenceTaxonomy 2021-02-22T23:02:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438931-AS-FisherStrand 2021-02-22T23:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438951-CompareBaseQualities 2021-02-22T23:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360057438971-BwaSpark-BETA 2021-02-22T23:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439011-AnnotateVcfWithBamDepth 2021-02-22T23:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439031-MarkDuplicatesWithMateCigar-Picard 2021-02-22T23:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439051-PathSeqBuildKmers 2021-02-22T23:06:46Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439071-IntervalListTools-Picard 2021-02-22T23:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439091-StrandBiasBySample 2021-02-22T23:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439111-LearnReadOrientationModel 2021-02-22T23:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439131-CollectReadCounts 2021-02-22T23:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439151-MappingQualityRankSumTest 2021-02-22T23:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439171-MappingQualityNotZeroReadFilter 2021-02-22T23:03:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439191-CollectJumpingLibraryMetrics-Picard 2021-02-22T23:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439211-SplitSamByNumberOfReads-Picard 2021-02-22T23:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439231-MateDifferentStrandReadFilter 2021-02-22T23:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439251-NonNFastaSize-Picard 2021-02-22T23:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439271-BaseRecalibratorSpark-BETA 2021-02-22T23:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439291-SelectVariants 2021-02-22T23:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439311-MappingQualityReadFilter 2021-02-22T23:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439331-GenomicsDBImport 2022-10-06T09:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439351-PrintReads 2021-02-22T23:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439371-MateDistantReadFilter 2021-02-22T23:07:00Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439391-ValidAlignmentStartReadFilter 2021-02-22T23:07:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439411-ReadsPipelineSpark-BETA 2021-04-03T11:46:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439431-CountFalsePositives-BETA 2021-02-22T23:07:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439451-VcfToIntervalList-Picard 2021-02-22T23:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439471-MarkIlluminaAdapters-Picard 2021-02-22T23:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439491-SampleList 2021-02-22T23:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439511-MeanQualityByCycleSpark-BETA 2021-02-22T23:07:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439531-FragmentLength 2021-02-22T23:03:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439551-CheckIlluminaDirectory-Picard 2021-02-22T23:07:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439571-CollectTargetedPcrMetrics-Picard 2021-02-22T23:07:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439591-ReblockGVCF-BETA 2021-02-22T23:07:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439611-MergeBamAlignment-Picard 2021-02-22T23:03:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439631-ModelSegments 2021-02-22T23:03:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439651-RevertSamSpark-BETA 2021-02-22T23:07:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439671-AmbiguousBaseReadFilter 2021-02-22T23:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439691-BedToIntervalList-Picard 2021-02-22T23:07:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439711-RemoveNearbyIndels 2021-02-22T23:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439731-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2021-02-22T23:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439751-OriginalAlignment 2021-02-22T23:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439771-MarkDuplicates-Picard 2021-04-13T10:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439791-CreateSequenceDictionary-Picard 2021-02-22T23:07:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439811-VcfToAdpc-Picard 2021-02-22T23:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439831-ReorderSam-Picard 2021-02-22T23:04:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439851-NotSupplementaryAlignmentReadFilter 2021-02-22T23:04:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439871-GenotypeSummaries 2021-02-22T23:04:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439891-FlagStatSpark 2021-02-22T23:07:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439911-FilterAlignmentArtifacts-EXPERIMENTAL 2021-05-30T14:33:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439931-CollectWgsMetrics-Picard 2021-02-22T23:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439951-PairedReadFilter 2021-02-22T23:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439971-AS-ReadPosRankSumTest 2021-02-22T23:04:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360057439991-FifoBuffer-Picard 2021-02-22T23:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440011-ExcessHet 2021-02-22T23:04:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440031-VariantFiltration 2021-02-22T23:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440051-LikelihoodRankSumTest 2021-02-22T23:04:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440071-RevertBaseQualityScores 2021-02-22T23:07:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440091-CompareSAMs-Picard 2021-02-22T23:07:32Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440111-PossibleDeNovo 2021-02-22T23:04:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440131-CollectInsertSizeMetricsSpark-BETA 2021-02-22T23:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440151-DenoiseReadCounts 2021-02-22T23:04:20Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440171-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2021-02-22T23:07:36Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440191-PrintSVEvidence-EXPERIMENTAL 2021-02-22T23:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440211-GermlineCNVCaller 2021-02-22T23:04:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440231-UpdateVcfSequenceDictionary-Picard 2021-02-22T23:04:26Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440251-ScatterIntervalsByNs-Picard 2021-02-22T23:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440271-AS-InbreedingCoeff 2021-02-22T23:04:30Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440311-VcfFormatConverter-Picard 2021-02-22T23:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440331-AddOrReplaceReadGroups-Picard 2021-02-22T23:04:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440351-CollectGcBiasMetrics-Picard 2021-02-22T23:04:38Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440371-ReadPosition 2021-02-22T23:04:40Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440391-Coverage 2021-02-22T23:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440411-ReadStrandFilter 2021-02-22T23:04:42Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440431-ApplyBQSRSpark-BETA 2021-03-12T14:40:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440451-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2021-02-22T23:04:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440471-CalculateGenotypePosteriors 2021-02-22T23:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440491-CollectMultipleMetrics-Picard 2021-02-22T23:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440511-MethylationTypeCaller-EXPERIMENTAL 2021-02-22T23:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440531-PreprocessIntervals 2021-02-22T23:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440551-FlagStat 2021-02-22T23:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440571-CombineGenotypingArrayVcfs-Picard 2021-02-22T23:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440591-InbreedingCoeff 2021-02-22T23:04:55Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440611-ValidateSamFile-Picard 2021-02-22T23:04:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440631-BpmToNormalizationManifestCsv-Picard 2021-02-22T23:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440651-FastqToSam-Picard 2021-02-22T23:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440671-SortSam-Picard 2021-02-22T23:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440691-CollectIlluminaBasecallingMetrics-Picard 2021-02-22T23:05:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440711-FuncotatorDataSourceDownloader 2021-02-22T23:05:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440731-ConvertHeaderlessHadoopBamShardToBam-BETA 2021-02-22T23:05:06Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440751-MergeSamFiles-Picard 2021-02-22T23:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440771-CollectRnaSeqMetrics-Picard 2021-02-22T23:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440791-PathSeqScoreSpark 2021-02-22T23:08:04Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440811-RevertSam-Picard 2021-02-22T23:08:05Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440831-PassesVendorQualityCheckReadFilter 2021-02-22T23:05:11Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440851-AS-MappingQualityRankSumTest 2021-02-22T23:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440871-BaseQuality 2021-02-22T23:05:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440891-SeqIsStoredReadFilter 2021-02-22T23:05:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440911-IntervalOverlapReadFilter 2021-02-22T23:05:15Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440931-NonZeroReferenceLengthAlignmentReadFilter 2021-02-22T23:05:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440951-CollectBaseDistributionByCycleSpark-BETA 2021-02-22T23:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440971-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2021-02-22T23:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/360057440991-FastaAlternateReferenceMaker 2021-02-22T23:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441011-UnmarkDuplicates 2021-02-22T23:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441031-StructuralVariationDiscoveryPipelineSpark-BETA 2021-02-22T23:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441051-EvaluateInfoFieldConcordance-BETA 2021-02-22T23:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441071-NonZeroFragmentLengthReadFilter 2021-02-22T23:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441091-PileupSpark-BETA 2021-02-22T23:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441111-ProperlyPairedReadFilter 2021-02-22T23:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441131-FilterFuncotations-EXPERIMENTAL 2021-02-22T23:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441151-CrosscheckFingerprints-Picard 2021-02-22T23:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441171-CNNVariantTrain-EXPERIMENTAL 2021-02-22T23:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441191-FindBadGenomicKmersSpark-BETA 2021-02-22T23:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441231-AddCommentsToBam-Picard 2021-02-22T23:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441251-Concordance 2021-02-22T23:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441291-CollectRrbsMetrics-Picard 2021-02-22T23:05:41Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441311-FindMendelianViolations-Picard 2021-02-22T23:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441331-ReferenceBases 2021-02-22T23:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441351-IndexFeatureFile 2021-02-22T23:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441371-ValidAlignmentEndReadFilter 2021-02-22T23:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441391-DepthPerSampleHC 2021-02-22T23:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441411-OrientationBiasReadCounts 2021-02-22T23:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441431-CountNs 2021-02-22T23:05:50Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441451-CollectOxoGMetrics-Picard 2021-02-22T23:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441471-CreateReadCountPanelOfNormals 2021-02-22T23:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441491-CollectDuplicateMetrics-Picard 2021-02-22T23:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441511-CountBasesSpark 2021-02-22T23:08:33Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441531-PrintReadsSpark 2021-02-22T23:08:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441551-ASEReadCounter 2021-02-22T23:08:34Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441571-CalibrateDragstrModel-BETA 2021-07-27T16:36:18Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441591-CreateSomaticPanelOfNormals-BETA 2021-02-22T23:08:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441611-CheckPileup 2021-02-22T23:08:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441631-GtcToVcf-Picard 2021-02-22T23:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441651-CheckTerminatorBlock-Picard 2021-02-22T23:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/360057441671-ReadLengthReadFilter 2021-02-22T23:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/360057630052-From-GATK-4-1-to-4-2-Two-years-of-updates-in-a-nutshell 2024-07-01T17:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/360057893792-Running-GATK-on-the-cloud-Overview 2024-06-25T07:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/360059164932--Mutect2-Webinar-Nov-17-2020 2024-11-09T06:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/360060004292-Introducing-GATK-for-Microbes 2026-01-06T14:33:45Z https://gatk.broadinstitute.org/hc/en-us/articles/360061483952-Known-Issue-with-Funcotator-Germline-v1-6-Data-Sources 2024-06-25T07:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR 2026-02-06T14:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4403687183515--How-to-Generate-an-unmapped-BAM-from-FASTQ-or-aligned-BAM 2024-07-31T08:26:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels 2025-05-27T13:06:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604554779-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2021-08-03T16:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604558235-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2021-08-03T16:47:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604559899-NonChimericOriginalAlignmentReadFilter 2021-08-03T16:47:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604561819-GenotypeConcordance-Picard 2021-08-03T16:52:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604563355-Pileup 2021-08-03T16:52:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604564635-OverclippedReadFilter 2021-08-03T16:47:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604565915-BwaMemIndexImageCreator 2021-08-03T16:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604567323-NotProperlyPairedReadFilter 2021-08-03T16:47:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604568347-WellformedReadFilter 2021-08-03T16:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604569499-SampleReadFilter 2021-08-03T16:48:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604570779-AnalyzeCovariates 2021-08-03T16:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604572059-RMSMappingQuality 2021-08-03T16:48:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604573851-Funcotator 2021-08-03T16:52:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604575771-PathSeqPipelineSpark 2021-08-03T16:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604577307-AlignmentAgreesWithHeaderReadFilter 2021-08-03T16:48:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604578843-AS-StrandOddsRatio 2021-08-03T16:48:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604580123-FilterVcf-Picard 2021-08-03T16:48:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604582043-CountReads 2021-08-03T16:52:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604590363-GnarlyGenotyper-BETA 2021-08-03T16:52:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604593563-PrintReadsHeader 2021-08-03T16:52:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604595099-ViewSam-Picard 2021-08-03T16:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604597659-CountVariants 2021-08-03T16:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604599067-AllowAllReadsReadFilter 2021-08-03T16:48:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604601371-NotDuplicateReadFilter 2021-08-03T16:48:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604602907-FilterSamReads-Picard 2021-08-03T16:53:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604604187-MergePedIntoVcf-Picard 2021-08-03T16:48:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604605339-PrimaryLineReadFilter 2021-08-03T16:48:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604606491-CollectMultipleMetricsSpark-BETA 2021-08-03T16:53:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604607515-CountBases 2021-08-03T16:53:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604608795-StrandOddsRatio 2021-08-03T16:48:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604609947--Tool-Documentation-Index 2021-08-03T16:53:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604610971-CheckFingerprint-Picard 2021-08-03T16:48:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604612251-HasReadGroupReadFilter 2021-08-03T16:48:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604613275-DetermineGermlineContigPloidy 2021-08-03T16:48:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604614811-MappingQuality 2021-08-03T16:48:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604615963-QualByDepth 2021-08-03T16:48:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604617115-VariantsToTable 2021-08-03T16:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604618139-NormalizeFasta-Picard 2021-08-03T16:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604619163-AS-RMSMappingQuality 2021-08-03T16:48:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604620955-CountVariantsSpark 2021-08-03T16:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604622107-UpdateVCFSequenceDictionary 2021-08-03T16:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604623259-IlluminaBasecallsToFastq-Picard 2021-08-03T16:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604624667-FisherStrand 2021-08-03T16:48:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604626843-CollectSamErrorMetrics-Picard 2021-08-03T16:48:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604628251-SoftClippedReadFilter 2021-08-03T16:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604629787-GetSampleName 2021-08-03T16:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604630939-DepthPerAlleleBySample 2021-08-03T16:48:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604631963-CalculateReadGroupChecksum-Picard 2021-08-03T16:53:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604633627-CompareMetrics-Picard 2021-08-03T16:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604635291-FuncotateSegments-BETA 2021-08-03T16:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604636827-GatherBamFiles-Picard 2021-08-03T16:49:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604638747-PathSeqBuildReferenceTaxonomy 2021-08-03T16:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604640283-AS-FisherStrand 2021-08-03T16:49:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604641947-BwaSpark-BETA 2021-08-03T16:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604645275-CollectSequencingArtifactMetrics-Picard 2021-08-03T16:49:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604647451-MappedReadFilter 2021-08-03T16:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604648475-ExtractSequences-Picard 2021-08-03T16:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604649883-MarkDuplicatesWithMateCigar-Picard 2021-08-03T16:53:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604651163-GatherBQSRReports 2021-08-03T16:49:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604652571-CalculateContamination 2021-08-03T16:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604653979-ApplyBQSR 2021-08-03T16:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604655771-CpxVariantReInterpreterSpark-BETA 2021-08-03T16:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604657051-MakeSitesOnlyVcf-Picard 2021-08-03T16:53:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604658331-IntervalListTools-Picard 2021-08-03T16:53:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604660123-CollectInsertSizeMetrics-Picard 2021-08-03T16:49:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604661147-StrandBiasBySample 2021-08-13T06:51:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604663323-LeftAlignIndels 2021-08-03T16:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604665243-FilterIntervals 2021-08-03T16:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604666267-MappingQualityRankSumTest 2021-08-03T16:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604667291-MappingQualityNotZeroReadFilter 2021-08-03T16:49:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604668571-HaplotypeCallerSpark-BETA 2021-08-03T16:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604669851-CollectJumpingLibraryMetrics-Picard 2021-08-03T16:49:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604671387-SplitSamByNumberOfReads-Picard 2021-08-03T16:53:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604672667-MateDifferentStrandReadFilter 2021-08-03T16:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604674075-NonNFastaSize-Picard 2021-08-03T16:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604675867-BaseRecalibratorSpark-BETA 2021-08-03T16:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604677275-CalculateMixingFractions 2021-08-03T16:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604678299-SelectVariants 2021-08-03T16:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604679323-AccumulateVariantCallingMetrics-Picard 2021-08-03T16:49:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604680603-IlluminaBasecallsToSam-Picard 2021-08-03T16:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604681883-ReadGroupReadFilter 2021-08-03T16:49:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604682907-MappingQualityReadFilter 2021-08-03T16:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604684443-CollectQualityYieldMetricsSpark-BETA 2021-08-03T16:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604685723-PlatformUnitReadFilter 2021-08-03T16:49:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604687387-CreateBafRegressMetricsFile-Picard 2021-08-03T16:49:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604688667-CreateHadoopBamSplittingIndex-BETA 2021-08-03T16:49:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604691099-PrintReads 2021-08-03T16:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604694555-BwaAndMarkDuplicatesPipelineSpark-BETA 2021-08-03T16:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604695835-MateDistantReadFilter 2021-08-03T16:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604697243-HaplotypeCaller 2021-08-03T16:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604699419-ValidAlignmentStartReadFilter 2021-08-03T16:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604700955-ReadsPipelineSpark-BETA 2021-08-03T16:53:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604702363-ReplaceSamHeader-Picard 2021-08-03T16:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604703515-CountFalsePositives-BETA 2021-08-03T16:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604704923-MateUnmappedAndUnmappedReadFilter 2021-08-03T16:49:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604705947-CollectIlluminaLaneMetrics-Picard 2021-08-03T16:49:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604707227-CountBasesInReference 2021-08-03T16:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604708251-VcfToIntervalList-Picard 2021-08-03T16:53:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604710683-MarkIlluminaAdapters-Picard 2021-08-03T16:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604714779-MatchingBasesAndQualsReadFilter 2021-08-03T16:49:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604718363-MeanQualityByCycleSpark-BETA 2021-08-03T16:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604720155-FragmentLength 2021-08-03T16:50:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604721563-CheckIlluminaDirectory-Picard 2021-08-03T16:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604722715-CollectTargetedPcrMetrics-Picard 2021-08-03T16:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604724891-MergeBamAlignment-Picard 2021-08-03T16:50:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604727067-FixMisencodedBaseQualityReads 2021-08-03T16:54:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604730011-LeftAlignAndTrimVariants 2021-08-03T16:54:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604732315-FeaturizedReadSets 2021-08-03T16:50:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604733979-ExtractIlluminaBarcodes-Picard 2021-08-03T16:50:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604735131-AmbiguousBaseReadFilter 2021-08-03T16:50:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604736411-BedToIntervalList-Picard 2021-08-03T16:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604737819-RemoveNearbyIndels 2021-08-03T16:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604738971-CompareDuplicatesSpark-BETA 2021-08-03T16:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604742683-MarkDuplicates-Picard 2021-08-03T16:50:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604743707-CreateSequenceDictionary-Picard 2021-08-03T16:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604744859-GoodCigarReadFilter 2021-08-03T16:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604745883-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-08-03T16:50:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604747291-AllelePseudoDepth 2021-08-03T16:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604748315-PositionBasedDownsampleSam-Picard 2021-08-03T16:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604749979-ReorderSam-Picard 2021-08-03T16:50:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604751259-NotSupplementaryAlignmentReadFilter 2021-08-03T16:50:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604752283-GenotypeSummaries 2021-08-03T16:50:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604753691-FlagStatSpark 2021-08-03T16:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604754971-FilterAlignmentArtifacts-EXPERIMENTAL 2021-08-03T16:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604756635-CollectWgsMetrics-Picard 2021-08-03T16:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604758299-PairedReadFilter 2021-08-03T16:50:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604759579-AS-ReadPosRankSumTest 2021-08-03T16:50:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604761499-FifoBuffer-Picard 2021-08-03T16:50:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604763547-VariantFiltration 2021-08-03T16:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604765467-BaseRecalibrator 2021-08-03T16:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604767003-RevertBaseQualityScores 2021-08-03T16:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604768283-GatherTranches-BETA 2021-08-03T16:50:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604771227-DownsampleSam-Picard 2021-08-03T16:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604772251-ClippingRankSumTest 2021-08-03T16:50:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604773659-CompareSAMs-Picard 2021-08-03T16:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604775451-BQSRPipelineSpark-BETA 2021-08-03T16:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604776731-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-08-03T16:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604777883-PossibleDeNovo 2021-08-03T16:50:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604780059-DenoiseReadCounts 2021-08-03T16:50:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604784283-BaseQualityRankSumTest 2021-08-03T16:50:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604786331-ApplyVQSR 2021-08-03T16:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604787611-PrintSVEvidence-EXPERIMENTAL 2021-08-03T16:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604788891-GermlineCNVCaller 2021-08-03T16:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604791067-MappingQualityZero 2021-08-03T16:50:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604792731-ScatterIntervalsByNs-Picard 2021-08-03T16:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604793755-AS-InbreedingCoeff 2021-08-03T16:50:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604795035-BamIndexStats-Picard 2021-08-03T16:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604796187-Mutect2 2021-08-03T16:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604797211-CollectArraysVariantCallingMetrics-Picard 2021-08-03T16:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604799771-PlotModeledSegments 2021-08-03T16:50:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604800923-CollectVariantCallingMetrics-Picard 2021-08-03T16:50:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604801947-CombineGVCFs 2021-08-03T16:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604806683-LocalAssembler-BETA 2021-08-03T16:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604808219-CollectGcBiasMetrics-Picard 2021-08-03T16:51:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604813211-AddOATag-Picard 2021-08-03T16:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604814491-ReadPosition 2021-08-03T16:51:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604815643-Coverage 2021-08-03T16:51:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604816923-ReadStrandFilter 2021-08-03T16:51:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604818331-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2021-08-03T16:51:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604819355-CalculateGenotypePosteriors 2021-08-03T16:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604820891-MergeVcfs-Picard 2021-08-03T16:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604821915-CollectMultipleMetrics-Picard 2021-08-03T16:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604822939-ValidateVariants 2021-08-03T16:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604824859-CollectAllelicCounts 2021-08-03T16:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604826395-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2021-08-03T16:51:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604827931-MethylationTypeCaller-EXPERIMENTAL 2021-08-03T16:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604828955-PreprocessIntervals 2021-08-03T16:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604830747-QualityScoreDistribution-Picard 2021-08-03T16:51:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604832283-PrintDistantMates 2021-08-03T16:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604834075-FlagStat 2021-08-03T16:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604835099-CombineGenotypingArrayVcfs-Picard 2021-08-03T16:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604836891-BaitDesigner-Picard 2021-08-03T16:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604838299-InbreedingCoeff 2021-08-03T16:51:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604839451-ReadLengthEqualsCigarLengthReadFilter 2021-08-03T16:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604840731-SortVcf-Picard 2021-08-03T16:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604842011-PrintVariantsSpark 2021-08-03T16:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604843163-BpmToNormalizationManifestCsv-Picard 2021-08-03T16:55:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604844187-FastqToSam-Picard 2021-08-03T16:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604848411-ReadGroupBlackListReadFilter 2021-08-03T16:51:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604849819-SamToFastq-Picard 2021-08-03T16:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604850843-SortSam-Picard 2021-08-03T16:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604853019-ConvertHeaderlessHadoopBamShardToBam-BETA 2021-08-03T16:51:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604854299-MergeSamFiles-Picard 2021-08-03T16:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604855579-CollectRnaSeqMetrics-Picard 2021-08-03T16:51:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604858011-PassesVendorQualityCheckReadFilter 2021-08-03T16:51:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604862747-ReadPosRankSumTest 2021-08-03T16:51:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604864539-BaseQuality 2021-08-03T16:51:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604866075-SeqIsStoredReadFilter 2021-08-03T16:51:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604869915-IntervalOverlapReadFilter 2021-08-03T16:51:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604871579-NonZeroReferenceLengthAlignmentReadFilter 2021-08-03T16:51:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604873243-VariantRecalibrator 2021-08-03T16:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604878107-PathSeqFilterSpark 2021-08-03T16:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604879387-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2021-08-03T16:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604881563-PlotDenoisedCopyRatios 2021-08-03T16:51:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604884251-FastaAlternateReferenceMaker 2021-08-03T16:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604885659-UnmarkDuplicates 2021-08-03T16:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604888731-SplitNCigarReads 2021-08-03T16:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604889883-NonZeroFragmentLengthReadFilter 2021-08-03T16:51:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604891035-DepthOfCoverage-BETA 2021-08-03T16:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604892315-PileupSpark-BETA 2021-08-03T16:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604893467-CigarContainsNoNOperator 2021-08-03T16:51:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604895771-FilterFuncotations-EXPERIMENTAL 2021-08-03T16:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604897179-CrosscheckFingerprints-Picard 2021-08-03T16:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604898331-CNNVariantTrain-EXPERIMENTAL 2021-08-03T16:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604900251-TandemRepeat 2021-08-03T16:52:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604901787-FindBadGenomicKmersSpark-BETA 2021-08-03T16:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604903451-AnalyzeSaturationMutagenesis-BETA 2021-08-03T16:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604904603-AS-BaseQualityRankSumTest 2021-08-03T16:52:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604906139-Concordance 2021-08-03T16:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604907419-FragmentLengthReadFilter 2021-08-03T16:52:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604908443-BuildBamIndex-Picard 2021-08-03T16:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604910107-FindMendelianViolations-Picard 2021-08-03T16:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604911259-ShiftFasta-BETA 2021-08-03T16:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604912283-ReferenceBases 2021-08-03T16:52:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604914075-IndexFeatureFile 2021-08-03T16:52:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604916635-QualityScoreDistributionSpark-BETA 2021-08-03T16:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604918043-DepthPerSampleHC 2021-08-03T16:52:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604919323-AlleleFraction 2021-08-03T16:52:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604920859-ConvertSequencingArtifactToOxoG-Picard 2021-08-03T16:52:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604922011-OrientationBiasReadCounts 2021-08-03T16:52:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604927259-AssemblyComplexity 2021-08-03T16:52:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604929179-RenameSampleInVcf-Picard 2021-08-03T16:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604930459-ReadAnonymizer-EXPERIMENTAL 2021-08-03T16:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604932379-CollectOxoGMetrics-Picard 2021-08-03T16:52:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604933659-CreateReadCountPanelOfNormals 2021-08-03T16:52:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604934939-CollectDuplicateMetrics-Picard 2021-08-03T16:52:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604936475-CountBasesSpark 2021-08-03T16:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604938395-PrintReadsSpark 2021-08-03T16:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604942747-ASEReadCounter 2021-08-03T16:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604943771-CalibrateDragstrModel 2021-08-03T16:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604945179-CreateSomaticPanelOfNormals-BETA 2021-08-03T16:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604946331-CheckPileup 2021-08-03T16:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604947355-GtcToVcf-Picard 2021-08-03T16:52:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4404604948635-ReadLengthReadFilter 2021-08-03T16:52:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607453723-ChromosomeCounts 2021-08-03T16:47:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607455003-LibraryReadFilter 2021-08-03T16:47:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607457819-MeanQualityByCycle-Picard 2021-08-03T16:52:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607458971-CollectHiSeqXPfFailMetrics-Picard 2021-08-03T16:47:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607462811-FirstOfPairReadFilter 2021-08-03T16:48:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607463835-CollectQualityYieldMetrics-Picard 2021-08-03T16:48:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607464987-CalcMetadataSpark-BETA 2021-08-03T16:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607466139-SecondOfPairReadFilter 2021-08-03T16:48:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607467547-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2021-08-03T16:52:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607468955-VariantEval-BETA 2021-08-03T16:48:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607470747-FixVcfHeader-Picard 2021-08-03T16:52:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607472027-CollectHsMetrics-Picard 2021-08-03T16:52:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607474331-EstimateLibraryComplexity-Picard 2021-08-03T16:48:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607476635-AnnotateVcfWithExpectedAlleleFraction 2021-08-03T16:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607478171-LiftOverIntervalList-Picard 2021-08-03T16:48:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607479451-BamToBfq-Picard 2021-08-03T16:48:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607480859-VariantAnnotator 2021-08-03T16:53:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607482907-FindBreakpointEvidenceSpark-BETA 2021-08-03T16:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607483803-UniqueAltReadCount 2021-08-03T16:48:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607484955-CNNVariantWriteTensors-EXPERIMENTAL 2021-08-03T16:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607486107-SamFormatConverter-Picard 2021-08-03T16:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607487515-GeneExpressionEvaluation-BETA 2021-08-03T16:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607488667-ClusterCrosscheckMetrics-Picard 2021-08-03T16:48:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607490075-ClipReads 2021-08-03T16:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607491355-MarkDuplicatesSpark 2021-08-03T16:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607492251-SetNmMdAndUqTags-Picard 2021-08-03T16:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607493915-CalculateFingerprintMetrics-Picard 2021-08-03T16:49:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607495323-CompareBaseQualities 2021-08-03T16:49:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607496347-CollectAlignmentSummaryMetrics-Picard 2021-08-03T16:49:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607497371-AnnotateVcfWithBamDepth 2021-08-03T16:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607498523-GatherVcfs-Picard 2021-08-03T16:49:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607502107-PathSeqBuildKmers 2021-08-03T16:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607504923-LearnReadOrientationModel 2021-08-03T16:49:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607505819-CollectReadCounts 2021-08-03T16:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607507227-SortSamSpark-BETA 2021-08-03T16:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607509403-FilterMutectCalls 2025-04-08T23:01:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607512475-GenomicsDBImport 2021-08-03T16:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607517851-SetNmAndUqTags-Picard 2021-08-03T16:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607519259-PathSeqBwaSpark 2021-08-03T16:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607520539-SampleList 2021-08-03T16:49:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607521819-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2021-08-03T16:53:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607523995-CollectBaseDistributionByCycle-Picard 2021-08-03T16:50:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607524891-ReblockGVCF-BETA 2023-08-24T12:10:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607526811-ModelSegments 2021-08-03T16:54:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607527835-RevertSamSpark-BETA 2021-08-03T16:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607529499-CollectRawWgsMetrics-Picard 2021-08-03T16:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607530907-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2021-08-03T16:54:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607532187-OriginalAlignment 2021-08-03T16:50:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607533467-VcfToAdpc-Picard 2021-08-03T16:50:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607536155-PostprocessGermlineCNVCalls 2021-08-03T16:54:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607537947-GetPileupSummaries 2021-08-03T16:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607540379-ExcessHet 2021-08-03T16:50:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607541787-LikelihoodRankSumTest 2021-08-03T16:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607545627-CollectInsertSizeMetricsSpark-BETA 2021-08-03T16:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607547931-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2021-08-03T16:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607549339-IntervalListToBed-Picard 2021-08-03T16:50:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607550747-UpdateVcfSequenceDictionary-Picard 2021-08-03T16:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607551771-ReadNameReadFilter 2021-08-03T16:50:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607552923-CallCopyRatioSegments 2021-08-03T16:50:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607554203-PlatformReadFilter 2021-08-03T16:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607556379-VcfFormatConverter-Picard 2021-08-03T16:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607557787-AddOrReplaceReadGroups-Picard 2021-08-03T16:50:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607560731-LiftoverVcf-Picard 2021-08-03T16:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607561627-MateOnSameContigOrNoMappedMateReadFilter 2021-08-03T16:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607562779-ApplyBQSRSpark-BETA 2021-08-03T16:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607564827-ExtractSVEvidenceSpark-BETA 2021-08-03T16:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607566107-CNNScoreVariants 2021-08-03T16:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607568027-FixMateInformation-Picard 2021-08-03T16:51:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607569691-ValidateSamFile-Picard 2021-08-03T16:51:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607571355-CollectIlluminaBasecallingMetrics-Picard 2021-08-03T16:51:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607572635-FuncotatorDataSourceDownloader 2021-08-03T16:51:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607574299-GatherVcfsCloud-BETA 2021-08-03T16:51:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607575451-AnnotateIntervals 2021-08-03T16:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607576987-PathSeqScoreSpark 2021-08-03T16:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607577883-RevertSam-Picard 2021-08-03T16:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607579035-SplitReads 2021-08-03T16:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607579931-AS-MappingQualityRankSumTest 2021-08-03T16:51:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607582363-CollectBaseDistributionByCycleSpark-BETA 2021-08-03T16:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607586331-SplitIntervals 2021-08-03T16:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607589915-StructuralVariationDiscoveryPipelineSpark-BETA 2021-08-03T16:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607591451-EvaluateInfoFieldConcordance-BETA 2021-08-03T16:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607593755-ProperlyPairedReadFilter 2021-08-03T16:51:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607595419-SplitVcfs-Picard 2021-08-03T16:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607597723-SplitSamByLibrary-Picard 2021-08-03T16:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607598875-GenotypeGVCFs 2021-08-03T16:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607600411-AddCommentsToBam-Picard 2021-08-03T16:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607601563-AS-QualByDepth 2021-08-03T16:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607603995-CollectRrbsMetrics-Picard 2021-08-03T16:52:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607605275-NotSecondaryAlignmentReadFilter 2021-08-03T16:52:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607606811-MetricsReadFilter 2021-08-03T16:52:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607607835-ValidAlignmentEndReadFilter 2021-08-03T16:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607609243-FastaReferenceMaker 2021-08-03T16:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607611931-CountNs 2021-08-03T16:52:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607612955-MappingQualityAvailableReadFilter 2021-08-03T16:52:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607615131-CountReadsSpark 2021-08-03T16:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607619227-FilterVariantTranches 2021-08-03T16:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607621147-CheckTerminatorBlock-Picard 2021-08-03T16:52:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4404607622171-CleanSam-Picard 2021-08-03T16:52:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4404707557915--GATK-4-2-1-0-release 2024-07-01T17:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443482907-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2021-08-19T16:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443484187-ChromosomeCounts 2021-08-19T16:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443486747-LibraryReadFilter 2021-08-19T16:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443487899-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2021-08-19T16:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443488795-NonChimericOriginalAlignmentReadFilter 2021-08-19T16:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443490203-MeanQualityByCycle-Picard 2021-08-19T16:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443491611-GenotypeConcordance-Picard 2021-08-19T16:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443492507-Pileup 2021-08-19T16:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443493659-BwaMemIndexImageCreator 2021-08-19T16:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443494811-WellformedReadFilter 2021-08-19T16:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443495963-SampleReadFilter 2021-08-19T16:53:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443497115-AnalyzeCovariates 2021-08-19T16:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443498395-RMSMappingQuality 2021-08-19T16:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443500699-PathSeqPipelineSpark 2021-08-19T16:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443502235-AlignmentAgreesWithHeaderReadFilter 2021-08-19T16:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443503387-AS-StrandOddsRatio 2021-08-19T16:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443504411-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2021-08-19T16:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443506459-CountReads 2021-08-19T16:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443510683-FixVcfHeader-Picard 2021-08-19T16:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443512091-GnarlyGenotyper-BETA 2021-08-19T16:57:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443513115-EstimateLibraryComplexity-Picard 2021-08-19T16:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443514267-ViewSam-Picard 2021-08-19T16:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443515163-AnnotateVcfWithExpectedAlleleFraction 2021-08-19T16:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443517339-BamToBfq-Picard 2021-08-19T16:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443523227-CountBases 2021-08-19T16:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443524763--Tool-Documentation-Index 2021-08-19T16:57:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443526299-CheckFingerprint-Picard 2021-08-19T16:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443527195-HasReadGroupReadFilter 2021-08-19T16:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443529755-CountVariantsSpark 2021-08-19T16:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443530907-UpdateVCFSequenceDictionary 2021-08-19T16:57:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443531803-IlluminaBasecallsToFastq-Picard 2021-08-19T16:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443532955-SamFormatConverter-Picard 2021-08-19T16:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443533851-FisherStrand 2021-08-19T16:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443534747-GeneExpressionEvaluation-BETA 2021-08-19T16:57:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443535899-ClipReads 2021-08-19T16:57:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443537051-CollectSamErrorMetrics-Picard 2021-08-19T16:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443537947-SoftClippedReadFilter 2021-08-19T16:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443539483-GetSampleName 2021-08-19T16:57:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443541787-CalculateReadGroupChecksum-Picard 2021-08-19T16:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443542683-SetNmMdAndUqTags-Picard 2021-08-19T16:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443543579-CompareMetrics-Picard 2021-08-19T16:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443547035-AS-FisherStrand 2021-08-19T16:53:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443547931-CompareBaseQualities 2021-08-19T16:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443549339-CollectAlignmentSummaryMetrics-Picard 2021-08-19T16:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443550235-CollectSequencingArtifactMetrics-Picard 2021-08-19T16:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443551131-GatherVcfs-Picard 2021-08-19T16:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443552155-MappedReadFilter 2021-08-19T16:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443553179-ExtractSequences-Picard 2021-08-19T16:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443554203-MarkDuplicatesWithMateCigar-Picard 2021-08-19T16:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443555483-GatherBQSRReports 2021-08-19T16:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443556763-PathSeqBuildKmers 2021-08-19T16:57:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443558299-MakeSitesOnlyVcf-Picard 2021-08-19T16:57:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443559707-CollectInsertSizeMetrics-Picard 2021-08-19T16:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443560987-CollectReadCounts 2021-08-19T16:57:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443566875-HaplotypeCallerSpark-BETA 2021-08-19T16:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443568027-CollectJumpingLibraryMetrics-Picard 2021-08-19T16:54:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443568923-SplitSamByNumberOfReads-Picard 2021-08-19T16:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443570587-NonNFastaSize-Picard 2021-08-19T16:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443576219-IlluminaBasecallsToSam-Picard 2021-08-19T16:54:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443577627-PlatformUnitReadFilter 2021-08-19T16:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443579035-CreateBafRegressMetricsFile-Picard 2021-08-19T16:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443581467-BwaAndMarkDuplicatesPipelineSpark-BETA 2021-08-19T16:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443582747-MateDistantReadFilter 2021-08-19T16:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443583899-ReadsPipelineSpark-BETA 2021-08-19T16:57:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443585947-CountFalsePositives-BETA 2021-08-19T16:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443587099-MateUnmappedAndUnmappedReadFilter 2021-08-19T16:54:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443592731-PathSeqBwaSpark 2021-08-19T16:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443594139-MarkIlluminaAdapters-Picard 2021-08-19T16:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443596187-MatchingBasesAndQualsReadFilter 2021-08-19T16:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443597467-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2021-08-19T16:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443598619-CheckIlluminaDirectory-Picard 2021-08-19T16:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443599643-CollectBaseDistributionByCycle-Picard 2021-08-19T16:54:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443600667-ReblockGVCF 2021-08-19T16:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443601947-MergeBamAlignment-Picard 2021-08-19T16:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443603483-FixMisencodedBaseQualityReads 2021-08-19T16:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443605531-LeftAlignAndTrimVariants 2024-02-20T11:24:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443607323-FeaturizedReadSets 2021-08-19T16:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443608603-AmbiguousBaseReadFilter 2021-08-24T17:13:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443613211-RemoveNearbyIndels 2021-08-19T16:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443614747-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2021-08-19T16:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443615771-MarkDuplicates-Picard 2021-08-19T16:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443616667-CreateSequenceDictionary-Picard 2021-08-19T16:58:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443617819-GoodCigarReadFilter 2021-08-19T16:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443619483-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-08-19T16:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443620379-AllelePseudoDepth 2021-08-19T16:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443621403-PositionBasedDownsampleSam-Picard 2021-08-19T16:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443623707-PostprocessGermlineCNVCalls 2021-08-19T16:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443624731-NotSupplementaryAlignmentReadFilter 2021-08-19T16:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443625755-GenotypeSummaries 2021-08-19T16:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443627035-FlagStatSpark 2021-08-19T16:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443627931-FilterAlignmentArtifacts-EXPERIMENTAL 2021-08-19T16:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443629595-AS-ReadPosRankSumTest 2021-08-19T16:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443630491-ExcessHet 2021-08-19T16:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443631643-LikelihoodRankSumTest 2021-08-19T16:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443632539-BaseRecalibrator 2021-08-19T16:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443633435-GatherTranches-BETA 2021-08-19T16:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443634587-DownsampleSam-Picard 2021-08-19T16:58:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443635611-ClippingRankSumTest 2021-08-19T16:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443636763-BQSRPipelineSpark-BETA 2021-08-19T16:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443638171-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-08-19T16:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443639323-PossibleDeNovo 2021-08-19T16:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443640731-CollectInsertSizeMetricsSpark-BETA 2021-08-19T16:58:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443642779-DenoiseReadCounts 2021-08-19T16:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443644315-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2021-08-19T16:58:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443646363-IntervalListToBed-Picard 2021-08-19T16:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443650331-PrintSVEvidence-EXPERIMENTAL 2021-08-19T16:58:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443651867-ReadNameReadFilter 2021-08-19T16:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443654683-PlatformReadFilter 2021-08-19T16:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443655835-BamIndexStats-Picard 2021-08-19T16:58:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443657499-Mutect2 2021-08-19T16:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443659547-CollectArraysVariantCallingMetrics-Picard 2021-08-19T16:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443660827-VcfFormatConverter-Picard 2021-08-19T16:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443662363-CombineGVCFs 2021-08-19T16:58:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443663259-LocalAssembler-BETA 2021-08-19T16:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443664155-CollectGcBiasMetrics-Picard 2021-08-19T16:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443665563-AddOATag-Picard 2021-08-19T16:58:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443666843-ReadPosition 2021-08-19T16:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443667739-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2021-08-19T16:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443668891-MergeVcfs-Picard 2021-08-19T16:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443670171-ValidateVariants 2021-08-19T16:58:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443671195-MethylationTypeCaller-EXPERIMENTAL 2021-08-19T16:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443672347-PreprocessIntervals 2021-08-19T16:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443673243-FlagStat 2021-08-19T16:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443674779-CombineGenotypingArrayVcfs-Picard 2021-08-19T16:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443675931-BaitDesigner-Picard 2021-08-19T16:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443677339-InbreedingCoeff 2021-08-19T16:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443678619-ReadLengthEqualsCigarLengthReadFilter 2021-08-19T16:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443680155-SortVcf-Picard 2021-08-19T16:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443686427-ValidateSamFile-Picard 2021-08-19T16:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443691675-ReadGroupBlackListReadFilter 2021-08-19T16:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443692571-SamToFastq-Picard 2021-08-19T16:58:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443699099-MergeSamFiles-Picard 2021-08-19T16:58:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443700763-GatherVcfsCloud-BETA 2021-08-19T16:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443703195-PassesVendorQualityCheckReadFilter 2021-08-19T16:55:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443704347-SplitReads 2021-08-19T16:58:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443705243-ReadPosRankSumTest 2021-08-19T16:56:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443706395-BaseQuality 2021-08-19T16:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443707675-SeqIsStoredReadFilter 2021-08-19T16:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443708699-CollectBaseDistributionByCycleSpark-BETA 2021-08-19T16:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443709595-VariantRecalibrator 2021-08-19T16:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443710747-PathSeqFilterSpark 2021-08-19T16:58:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443712283-PlotDenoisedCopyRatios 2021-08-19T16:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443713435-SplitIntervals 2021-08-19T16:58:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443715611-StructuralVariationDiscoveryPipelineSpark-BETA 2021-08-19T16:58:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443716763-EvaluateInfoFieldConcordance-BETA 2021-08-19T16:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443717659-SplitNCigarReads 2021-08-19T16:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443719195-NonZeroFragmentLengthReadFilter 2021-08-19T16:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443721243-PileupSpark-BETA 2021-08-19T16:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443722651-ProperlyPairedReadFilter 2021-08-19T16:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443723547-CigarContainsNoNOperator 2021-08-19T16:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443724443-SplitSamByLibrary-Picard 2021-08-19T16:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443726107-AnalyzeSaturationMutagenesis-BETA 2021-08-19T16:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443727003-AS-QualByDepth 2021-08-19T16:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443729051-CollectRrbsMetrics-Picard 2021-08-19T16:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443730331-FindMendelianViolations-Picard 2021-08-19T16:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443731355-ReferenceBases 2021-08-19T16:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443733147-ValidAlignmentEndReadFilter 2021-08-19T16:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443734299-FastaReferenceMaker 2021-08-19T16:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443735451-AlleleFraction 2021-08-19T16:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443738139-ReadAnonymizer-EXPERIMENTAL 2021-08-19T16:59:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443739419-MappingQualityAvailableReadFilter 2021-08-19T16:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443741595-CollectOxoGMetrics-Picard 2021-08-19T16:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443742491-CreateReadCountPanelOfNormals 2021-08-19T16:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443744411-ASEReadCounter 2021-08-19T16:59:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443745563-FilterVariantTranches 2021-08-19T16:59:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443746843-CheckPileup 2021-08-19T16:59:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4405443747739-GtcToVcf-Picard 2021-08-19T16:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451163931-CollectHiSeqXPfFailMetrics-Picard 2021-08-19T16:53:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451165595-OverclippedReadFilter 2021-08-19T16:53:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451166875-NotProperlyPairedReadFilter 2021-08-19T16:53:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451169435-FirstOfPairReadFilter 2021-08-19T16:53:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451170459-Funcotator 2021-08-19T16:56:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451171739-CollectQualityYieldMetrics-Picard 2021-08-19T16:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451173915-CalcMetadataSpark-BETA 2021-08-19T16:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451175067-SecondOfPairReadFilter 2021-08-19T16:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451176987-FilterVcf-Picard 2021-08-19T16:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451178139-VariantEval-BETA 2021-08-19T16:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451181083-CollectHsMetrics-Picard 2021-08-19T16:57:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451185819-PrintReadsHeader 2021-08-19T16:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451187739-CountVariants 2021-08-19T16:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451188763-AllowAllReadsReadFilter 2021-08-19T16:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451189787-LiftOverIntervalList-Picard 2021-08-19T16:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451190811-NotDuplicateReadFilter 2021-08-19T16:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451193115-VariantAnnotator 2021-08-19T16:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451195675-FilterSamReads-Picard 2021-08-19T16:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451197595-MergePedIntoVcf-Picard 2021-08-19T16:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451200539-PrimaryLineReadFilter 2021-08-19T16:53:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451202203-CollectMultipleMetricsSpark-BETA 2021-08-19T16:57:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451203355-StrandOddsRatio 2021-08-19T16:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451205019-DetermineGermlineContigPloidy 2021-08-19T16:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451206043-FindBreakpointEvidenceSpark-BETA 2021-08-19T16:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451207067-UniqueAltReadCount 2021-08-19T16:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451208091-MappingQuality 2021-08-19T16:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451209115-QualByDepth 2021-08-19T16:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451210139-VariantsToTable 2021-08-19T16:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451211291-NormalizeFasta-Picard 2021-08-19T16:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451212699-AS-RMSMappingQuality 2021-08-19T16:53:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451213979-CNNVariantWriteTensors-EXPERIMENTAL 2021-08-19T16:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451216411-ClusterCrosscheckMetrics-Picard 2021-08-19T16:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451219355-MarkDuplicatesSpark 2021-08-19T16:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451220635-DepthPerAlleleBySample 2021-08-19T16:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451222171-FuncotateSegments-BETA 2021-08-19T16:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451223195-GatherBamFiles-Picard 2021-08-19T16:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451224347-CalculateFingerprintMetrics-Picard 2021-08-19T16:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451225371-PathSeqBuildReferenceTaxonomy 2021-08-19T16:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451226779-BwaSpark-BETA 2021-08-19T16:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451228315-AnnotateVcfWithBamDepth 2021-08-19T16:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451230363-CalculateContamination 2021-08-19T16:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451231387-ApplyBQSR 2021-08-19T16:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451232411-CpxVariantReInterpreterSpark-BETA 2021-08-19T16:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451234331-IntervalListTools-Picard 2021-08-19T16:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451235867-StrandBiasBySample 2021-08-19T16:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451237147-LearnReadOrientationModel 2021-11-17T11:00:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451239323-SortSamSpark-BETA 2021-08-19T16:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451240475-LeftAlignIndels 2021-08-19T16:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451241883-FilterIntervals 2021-08-19T16:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451243291-MappingQualityRankSumTest 2021-08-19T16:54:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451244315-MappingQualityNotZeroReadFilter 2021-08-19T16:54:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451249819-ComposeSTRTableFile 2021-11-25T18:20:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451251355-MateDifferentStrandReadFilter 2021-08-19T16:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451253403-FilterMutectCalls 2021-08-19T16:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451255835-BaseRecalibratorSpark-BETA 2021-08-19T16:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451257115-CalculateMixingFractions 2021-08-19T16:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451258267-SelectVariants 2021-08-19T16:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451260443-AccumulateVariantCallingMetrics-Picard 2021-08-19T16:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451264155-ReadGroupReadFilter 2021-08-19T16:54:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451265179-MappingQualityReadFilter 2021-08-19T16:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451266331-GenomicsDBImport 2021-08-19T16:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451267355-CollectQualityYieldMetricsSpark-BETA 2021-08-19T16:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451269915-CreateHadoopBamSplittingIndex-BETA 2021-08-19T16:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451270939-PrintReads 2021-08-19T16:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451272731-HaplotypeCaller 2021-09-27T23:23:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451273883-ValidAlignmentStartReadFilter 2021-08-19T16:57:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451276315-ReplaceSamHeader-Picard 2021-08-19T16:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451278747-CollectIlluminaLaneMetrics-Picard 2021-08-19T16:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451280027-CountBasesInReference 2021-08-19T16:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451281435-VcfToIntervalList-Picard 2021-08-19T16:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451282587-SetNmAndUqTags-Picard 2021-08-19T16:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451285915-SampleList 2021-08-19T16:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451288091-MeanQualityByCycleSpark-BETA 2021-08-19T16:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451289243-FragmentLength 2021-08-19T16:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451290523-CollectTargetedPcrMetrics-Picard 2021-08-19T16:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451294747-ModelSegments 2021-08-19T16:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451296027-RevertSamSpark-BETA 2021-08-19T16:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451297051-ExtractIlluminaBarcodes-Picard 2021-08-19T16:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451298587-BedToIntervalList-Picard 2021-08-19T16:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451299867-CompareDuplicatesSpark-BETA 2021-08-19T16:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451301147-CollectRawWgsMetrics-Picard 2021-08-19T16:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451302555-OriginalAlignment 2021-08-19T16:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451304347-VcfToAdpc-Picard 2021-08-19T16:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451306907-ReorderSam-Picard 2021-08-19T16:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451309723-CollectWgsMetrics-Picard 2021-08-19T16:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451310875-PairedReadFilter 2021-08-19T16:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451312539-GetPileupSummaries 2021-08-19T16:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451313563-FifoBuffer-Picard 2021-08-19T16:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451314715-VariantFiltration 2021-08-19T16:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451318043-RevertBaseQualityScores 2021-08-19T16:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451320731-CompareSAMs-Picard 2021-08-19T16:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451324827-BaseQualityRankSumTest 2021-08-19T16:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451326619-ApplyVQSR 2021-08-19T16:58:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451329179-GermlineCNVCaller 2021-08-19T16:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451330587-UpdateVcfSequenceDictionary-Picard 2021-08-19T16:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451333403-MappingQualityZero 2021-08-19T16:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451334427-CallCopyRatioSegments 2021-08-19T16:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451335835-ScatterIntervalsByNs-Picard 2021-08-19T16:58:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451336859-AS-InbreedingCoeff 2021-08-19T16:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451340699-AddOrReplaceReadGroups-Picard 2021-08-19T16:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451341723-PlotModeledSegments 2021-08-19T16:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451342747-CollectVariantCallingMetrics-Picard 2021-08-19T16:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451345307-LiftoverVcf-Picard 2021-08-19T16:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451346587-MateOnSameContigOrNoMappedMateReadFilter 2021-08-19T16:58:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451347611-Coverage 2021-08-19T16:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451348635-ReadStrandFilter 2021-08-19T16:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451349787-ApplyBQSRSpark-BETA 2021-08-19T16:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451351835-CalculateGenotypePosteriors 2021-08-19T16:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451353243-CollectMultipleMetrics-Picard 2021-08-19T16:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451354395-ExtractSVEvidenceSpark-BETA 2021-08-19T16:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451355803-CollectAllelicCounts 2021-08-19T16:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451357083-CNNScoreVariants 2021-08-19T16:58:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451358235-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2021-08-19T16:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451359899-QualityScoreDistribution-Picard 2021-08-19T16:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451360923-PrintDistantMates 2021-08-19T16:58:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451362843-FixMateInformation-Picard 2021-08-19T16:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451363995-PrintVariantsSpark 2021-08-19T16:58:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451365147-BpmToNormalizationManifestCsv-Picard 2021-08-19T16:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451366171-FastqToSam-Picard 2021-08-19T16:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451368091-SortSam-Picard 2021-08-19T16:58:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451369243-CollectIlluminaBasecallingMetrics-Picard 2021-08-19T16:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451371547-FuncotatorDataSourceDownloader 2021-08-19T16:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451372571-ConvertHeaderlessHadoopBamShardToBam-BETA 2021-08-19T16:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451374107-CollectRnaSeqMetrics-Picard 2021-08-19T16:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451375259-AnnotateIntervals 2021-08-19T16:58:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451376795-PathSeqScoreSpark 2021-08-19T16:58:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451377947-RevertSam-Picard 2021-08-19T16:58:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451379739-AS-MappingQualityRankSumTest 2021-08-19T16:56:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451381531-IntervalOverlapReadFilter 2021-08-19T16:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451382683-NonZeroReferenceLengthAlignmentReadFilter 2021-08-19T16:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451384859-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2021-08-19T16:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451386395-FastaAlternateReferenceMaker 2021-08-19T16:58:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451387419-UnmarkDuplicates 2021-08-19T16:58:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451390619-DepthOfCoverage-BETA 2021-08-19T16:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451392411-SplitVcfs-Picard 2021-08-19T16:58:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451393691-FilterFuncotations-EXPERIMENTAL 2021-08-19T16:58:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451395483-CrosscheckFingerprints-Picard 2021-08-19T16:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451396635-CNNVariantTrain-EXPERIMENTAL 2021-08-19T16:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451397659-GenotypeGVCFs 2021-08-19T16:58:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451398811-TandemRepeat 2021-08-19T16:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451400475-FindBadGenomicKmersSpark-BETA 2021-08-19T16:59:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451401755-AddCommentsToBam-Picard 2021-08-19T16:59:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451403163-AS-BaseQualityRankSumTest 2021-08-19T16:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451404699-Concordance 2021-08-19T16:59:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451405723-FragmentLengthReadFilter 2021-08-19T16:56:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451406747-BuildBamIndex-Picard 2021-08-19T16:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451407899-NotSecondaryAlignmentReadFilter 2021-08-19T16:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451409051-ShiftFasta-BETA 2021-08-19T16:59:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451410459-IndexFeatureFile 2021-08-19T16:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451411611-MetricsReadFilter 2021-08-19T16:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451413403-QualityScoreDistributionSpark-BETA 2021-08-19T16:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451414683-DepthPerSampleHC 2021-08-19T16:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451416475-ConvertSequencingArtifactToOxoG-Picard 2021-08-19T16:56:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451417883-OrientationBiasReadCounts 2021-08-19T16:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451419035-AssemblyComplexity 2021-08-19T16:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451420059-CountNs 2021-08-19T16:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451421595-RenameSampleInVcf-Picard 2021-08-19T16:59:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451425435-CollectDuplicateMetrics-Picard 2021-08-19T16:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451426459-CountReadsSpark 2021-08-19T16:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451427483-CountBasesSpark 2021-08-19T16:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451428763-PrintReadsSpark 2021-08-19T16:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451430555-CalibrateDragstrModel 2021-08-19T16:59:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451431963-CreateSomaticPanelOfNormals-BETA 2024-01-24T12:31:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451433499-CheckTerminatorBlock-Picard 2021-08-19T16:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451434779-ReadLengthReadFilter 2021-08-19T16:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4405451435803-CleanSam-Picard 2021-08-19T16:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4405453519515--GATK-4-2-2-0-release 2024-07-01T17:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4406413438235-GATK-on-the-cloud-with-Terra 2024-06-25T07:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode 2024-07-31T08:24:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409678362139--GATK-4-2-3-0-release 2024-07-01T17:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897135771-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2021-11-08T23:05:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897137051-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2021-11-08T23:01:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897138331-OverclippedReadFilter 2021-11-08T23:01:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897139355-WellformedReadFilter 2021-11-08T23:05:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897141659-AnalyzeCovariates 2021-11-08T23:05:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897142555-RMSMappingQuality 2021-11-08T23:01:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897143707-FirstOfPairReadFilter 2021-11-08T23:01:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897144859-Funcotator 2021-11-08T23:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897146011-SecondOfPairReadFilter 2021-11-08T23:01:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897147035-AS-StrandOddsRatio 2021-11-08T23:01:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897148187-FixVcfHeader-Picard 2021-11-08T23:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897149211-EstimateLibraryComplexity-Picard 2021-11-08T23:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897150235-AnnotateVcfWithExpectedAlleleFraction 2021-11-08T23:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897151387-LiftOverIntervalList-Picard 2021-11-08T23:01:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897152283-NotDuplicateReadFilter 2021-11-08T23:01:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897153179-BamToBfq-Picard 2021-11-08T23:01:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897154971-StrandOddsRatio 2021-11-08T23:01:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897155995-DetermineGermlineContigPloidy 2021-11-08T23:01:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897158171-IlluminaBasecallsToFastq-Picard 2021-11-08T23:02:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897159195-GeneExpressionEvaluation-BETA 2021-11-08T23:06:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897160219-SoftClippedReadFilter 2021-11-08T23:02:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897161115-GetSampleName 2021-11-08T23:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897162139-MarkDuplicatesSpark 2021-11-08T23:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897163035-CalculateReadGroupChecksum-Picard 2021-11-08T23:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897164315-PathSeqBuildReferenceTaxonomy 2021-11-08T23:02:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897165595-CollectSequencingArtifactMetrics-Picard 2021-11-08T23:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897166619-MappedReadFilter 2021-11-08T23:02:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897167515-ExtractSequences-Picard 2021-11-08T23:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897168667-ApplyBQSR 2021-11-08T23:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897169563-CpxVariantReInterpreterSpark-BETA 2021-11-08T23:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897171227-CollectReadCounts 2021-11-08T23:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897172123-SortSamSpark-BETA 2021-11-08T23:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897173275-LeftAlignIndels 2021-11-08T23:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897174299-MappingQualityNotZeroReadFilter 2021-11-08T23:02:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897175451-SplitSamByNumberOfReads-Picard 2021-11-08T23:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897176987-SelectVariants 2021-11-08T23:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897178011-ReadGroupReadFilter 2021-11-08T23:02:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897179803-MateDistantReadFilter 2021-11-08T23:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897180827-HaplotypeCaller 2021-11-08T23:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897182107-CountFalsePositives-BETA 2021-11-08T23:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897183003-CollectIlluminaLaneMetrics-Picard 2021-11-08T23:03:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897184027-CountBasesInReference 2021-11-08T23:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897184923-VcfToIntervalList-Picard 2021-11-08T23:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897185947-PathSeqBwaSpark 2021-11-08T23:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897187099-MarkIlluminaAdapters-Picard 2024-10-30T15:32:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897188123-MatchingBasesAndQualsReadFilter 2021-11-08T23:03:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897189019-MeanQualityByCycleSpark-BETA 2021-11-08T23:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897190171-CheckIlluminaDirectory-Picard 2021-11-08T23:07:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897191451-ReblockGVCF 2021-11-08T23:07:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897192475-MergeBamAlignment-Picard 2021-11-08T23:03:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897193499-FixMisencodedBaseQualityReads 2021-11-08T23:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897194395-LeftAlignAndTrimVariants 2021-11-08T23:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897195675-RevertSamSpark-BETA 2021-11-08T23:07:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897196571-ExtractIlluminaBarcodes-Picard 2021-11-08T23:03:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897197595-RemoveNearbyIndels 2021-11-08T23:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897199259-OriginalAlignment 2021-11-08T23:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897201307-GetPileupSummaries 2021-11-08T23:07:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897202459-FifoBuffer-Picard 2021-11-08T23:03:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897203739-ExcessHet 2021-11-08T23:03:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897204763-VariantFiltration 2021-11-08T23:07:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897206043-BaseRecalibrator 2021-11-08T23:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897207323-DownsampleSam-Picard 2021-11-08T23:07:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897208219-ClippingRankSumTest 2021-11-08T23:03:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897209243-BQSRPipelineSpark-BETA 2021-11-08T23:07:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897210139-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-11-08T23:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897211419-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2021-11-08T23:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897212315-IntervalListToBed-Picard 2021-11-08T23:03:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897213339-GermlineCNVCaller 2021-11-08T23:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897214363-ReadNameReadFilter 2021-11-08T23:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897215387-CallCopyRatioSegments 2021-11-08T23:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897216283-ScatterIntervalsByNs-Picard 2021-11-08T23:07:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897217179-AS-InbreedingCoeff 2021-11-08T23:04:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897218459-AddOrReplaceReadGroups-Picard 2021-11-08T23:04:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897219611-PlotModeledSegments 2021-11-08T23:04:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897221019-CombineGVCFs 2021-11-08T23:07:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897222043-LocalAssembler-BETA 2021-11-08T23:07:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897222939-CollectGcBiasMetrics-Picard 2021-11-08T23:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897224219-Coverage 2021-11-08T23:04:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897225243-CalculateGenotypePosteriors 2021-11-08T23:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897226267-CollectMultipleMetrics-Picard 2021-11-08T23:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897227163-ValidateVariants 2021-11-08T23:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897228315-CollectAllelicCounts 2021-11-08T23:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897230107-FixMateInformation-Picard 2021-11-08T23:04:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897231259-SortVcf-Picard 2021-11-08T23:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897232155-PrintVariantsSpark 2021-11-08T23:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897233179-BpmToNormalizationManifestCsv-Picard 2021-11-08T23:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897234331-SamToFastq-Picard 2021-11-08T23:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897235355-FuncotatorDataSourceDownloader 2021-11-08T23:04:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897236507-MergeSamFiles-Picard 2021-11-08T23:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897237915-RevertSam-Picard 2021-11-08T23:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897239835-IntervalOverlapReadFilter 2021-11-08T23:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897240859-CollectBaseDistributionByCycleSpark-BETA 2021-11-08T23:08:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897241883-VariantRecalibrator 2021-11-08T23:08:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897242907-SplitIntervals 2021-11-08T23:08:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897244059-UnmarkDuplicates 2021-11-08T23:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897245339-ProperlyPairedReadFilter 2021-11-08T23:05:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897246235-CigarContainsNoNOperator 2021-11-08T23:05:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897247259-FilterFuncotations-EXPERIMENTAL 2021-11-08T23:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897248283-CrosscheckFingerprints-Picard 2021-11-08T23:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897249179-GenotypeGVCFs 2021-11-08T23:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897250203-TandemRepeat 2021-11-08T23:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897251355-AS-QualByDepth 2021-11-08T23:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897252379-FragmentLengthReadFilter 2021-11-08T23:05:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897253403-CollectRrbsMetrics-Picard 2021-11-08T23:05:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897254939-ValidAlignmentEndReadFilter 2021-11-08T23:08:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897255835-FastaReferenceMaker 2021-11-08T23:08:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897257371-CountNs 2021-11-08T23:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897258907-FilterVariantTranches 2021-11-08T23:08:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897260571-GtcToVcf-Picard 2021-11-08T23:05:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4409897261467-CheckTerminatorBlock-Picard 2021-11-08T23:05:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907926555-NonChimericOriginalAlignmentReadFilter 2021-11-08T23:01:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907927579-GenotypeConcordance-Picard 2021-11-08T23:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907929243-BwaMemIndexImageCreator 2021-11-08T23:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907930267-NotProperlyPairedReadFilter 2021-11-08T23:01:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907931931-SampleReadFilter 2021-11-08T23:01:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907933851-CollectQualityYieldMetrics-Picard 2021-11-08T23:01:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907934875-PathSeqPipelineSpark 2021-11-08T23:05:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907935899-CalcMetadataSpark-BETA 2021-11-08T23:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907937307-CollectHsMetrics-Picard 2021-11-08T23:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907938331-GnarlyGenotyper-BETA 2021-11-08T23:06:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907939995-AllowAllReadsReadFilter 2021-11-08T23:01:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907942043-FilterSamReads-Picard 2021-11-08T23:06:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907944219--Tool-Documentation-Index 2021-11-11T10:40:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907945243-CheckFingerprint-Picard 2021-11-08T23:01:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907946651-FindBreakpointEvidenceSpark-BETA 2021-11-08T23:06:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907948059-UniqueAltReadCount 2021-11-08T23:01:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907949083-MappingQuality 2021-11-08T23:01:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907950619-VariantsToTable 2021-11-08T23:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907951771-NormalizeFasta-Picard 2021-11-08T23:06:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907953051-CNNVariantWriteTensors-EXPERIMENTAL 2021-11-08T23:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907954203-CountVariantsSpark 2021-11-08T23:02:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907955995-SamFormatConverter-Picard 2021-11-08T23:02:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907957659-ClusterCrosscheckMetrics-Picard 2021-11-08T23:02:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907958811-ClipReads 2021-11-08T23:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907960475-SetNmMdAndUqTags-Picard 2021-11-08T23:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907961755-CompareMetrics-Picard 2021-11-08T23:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907963163-FuncotateSegments-BETA 2021-11-08T23:06:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907964187-CalculateFingerprintMetrics-Picard 2021-11-08T23:02:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907965979-AS-FisherStrand 2021-11-08T23:02:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907967387-CollectAlignmentSummaryMetrics-Picard 2021-11-08T23:02:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907968539-AnnotateVcfWithBamDepth 2021-11-08T23:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907971227-MarkDuplicatesWithMateCigar-Picard 2021-11-08T23:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907972891-PathSeqBuildKmers 2021-11-08T23:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907974299-CollectInsertSizeMetrics-Picard 2021-11-08T23:02:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907976219-LearnReadOrientationModel 2021-11-08T23:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907978267-CollectJumpingLibraryMetrics-Picard 2021-11-08T23:02:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907979931-ComposeSTRTableFile 2021-11-08T23:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907982619-BaseRecalibratorSpark-BETA 2021-11-08T23:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907986075-GenomicsDBImport 2021-11-08T23:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907987227-CollectQualityYieldMetricsSpark-BETA 2021-11-08T23:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907988251-PlatformUnitReadFilter 2021-11-08T23:02:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907989147-CreateHadoopBamSplittingIndex-BETA 2021-11-08T23:02:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907990171-PrintReads 2021-11-08T23:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907991323-BwaAndMarkDuplicatesPipelineSpark-BETA 2021-11-08T23:06:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907993499-MateUnmappedAndUnmappedReadFilter 2021-11-08T23:03:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907995931-SetNmAndUqTags-Picard 2021-11-08T23:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907998363-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2021-11-08T23:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4409907999771-CollectTargetedPcrMetrics-Picard 2021-11-08T23:07:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4409908000923-CollectBaseDistributionByCycle-Picard 2021-11-08T23:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917348891-ChromosomeCounts 2021-11-08T23:01:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917349915-LibraryReadFilter 2021-11-08T23:01:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917350939-MeanQualityByCycle-Picard 2021-11-08T23:05:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917352091-CollectHiSeqXPfFailMetrics-Picard 2021-11-08T23:01:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917353627-Pileup 2021-11-08T23:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917356827-AlignmentAgreesWithHeaderReadFilter 2021-11-08T23:01:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917357851-FilterVcf-Picard 2021-11-08T23:01:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917358747-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2021-11-08T23:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917359771-VariantEval-BETA 2021-11-08T23:01:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917360923-CountReads 2021-11-08T23:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917362331-PrintReadsHeader 2021-11-08T23:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917363227-ViewSam-Picard 2021-11-08T23:06:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917364507-CountVariants 2021-11-08T23:06:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917365659-VariantAnnotator 2021-11-08T23:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917366683-MergePedIntoVcf-Picard 2021-11-08T23:01:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917368347-PrimaryLineReadFilter 2021-11-08T23:01:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917369627-CollectMultipleMetricsSpark-BETA 2021-11-08T23:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917370651-CountBases 2021-11-08T23:06:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917372187-HasReadGroupReadFilter 2021-11-08T23:01:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917373723-QualByDepth 2021-11-08T23:01:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917374875-AS-RMSMappingQuality 2021-11-08T23:01:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917376923-UpdateVCFSequenceDictionary 2021-11-08T23:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917378331-FisherStrand 2021-11-08T23:02:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917379355-CollectSamErrorMetrics-Picard 2021-11-08T23:02:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917380891-DepthPerAlleleBySample 2021-11-08T23:02:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917382427-GatherBamFiles-Picard 2021-11-08T23:02:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917384603-CompareBaseQualities 2021-11-08T23:02:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917385755-BwaSpark-BETA 2021-11-08T23:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917386907-GatherVcfs-Picard 2021-11-08T23:02:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917388443-GatherBQSRReports 2021-11-08T23:02:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917389339-CalculateContamination 2021-11-08T23:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917391131-MakeSitesOnlyVcf-Picard 2021-11-08T23:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917392155-IntervalListTools-Picard 2021-11-08T23:06:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917393307-StrandBiasBySample 2021-11-08T23:02:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917394331-FragmentDepthPerAlleleBySample 2021-11-08T23:02:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917395611-FilterIntervals 2021-11-08T23:02:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917397147-MappingQualityRankSumTest 2021-11-08T23:02:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917402139-HaplotypeCallerSpark-BETA 2021-11-08T23:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917403419-MateDifferentStrandReadFilter 2021-11-08T23:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917404955-NonNFastaSize-Picard 2021-11-08T23:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917406107-FilterMutectCalls 2021-11-08T23:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917407259-CalculateMixingFractions 2021-11-08T23:06:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917408923-AccumulateVariantCallingMetrics-Picard 2021-11-08T23:02:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917410203-IlluminaBasecallsToSam-Picard 2021-11-08T23:02:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917411227-MappingQualityReadFilter 2021-11-08T23:06:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917412507-CreateBafRegressMetricsFile-Picard 2021-11-08T23:02:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917414171-ValidAlignmentStartReadFilter 2021-11-08T23:06:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917415195-ReadsPipelineSpark-BETA 2021-11-08T23:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917416091-ReplaceSamHeader-Picard 2021-11-08T23:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917418267-SampleList 2021-11-08T23:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917419931-FragmentLength 2021-11-08T23:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917421723-ModelSegments 2021-11-08T23:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917422619-FeaturizedReadSets 2021-11-08T23:03:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917423771-AmbiguousBaseReadFilter 2021-11-08T23:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917426075-CreateSequenceDictionary-Picard 2021-11-08T23:07:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917427355-VcfToAdpc-Picard 2021-11-08T23:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917429403-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-11-08T23:03:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917430939-AllelePseudoDepth 2021-11-08T23:03:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917431963-PositionBasedDownsampleSam-Picard 2021-11-08T23:03:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917433499-NotSupplementaryAlignmentReadFilter 2021-11-08T23:03:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917434395-FlagStatSpark 2021-11-08T23:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917435419-FilterAlignmentArtifacts-EXPERIMENTAL 2021-11-08T23:07:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917436315-CollectWgsMetrics-Picard 2021-11-08T23:03:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917437211-PairedReadFilter 2021-11-08T23:03:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917439003-LikelihoodRankSumTest 2021-11-08T23:03:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917441179-CompareSAMs-Picard 2021-11-08T23:07:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917442587-DenoiseReadCounts 2021-11-08T23:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917443611-BaseQualityRankSumTest 2021-11-08T23:03:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917445787-PlatformReadFilter 2021-11-08T23:04:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917446811-BamIndexStats-Picard 2021-11-08T23:07:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917447707-Mutect2 2021-11-08T23:07:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917448859-VcfFormatConverter-Picard 2021-11-08T23:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917450267-AddOATag-Picard 2021-11-08T23:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917451675-ReadStrandFilter 2021-11-08T23:04:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917453595-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2021-11-08T23:04:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917454491-MethylationTypeCaller-EXPERIMENTAL 2021-11-08T23:07:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917455515-PreprocessIntervals 2021-11-08T23:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917456539-QualityScoreDistribution-Picard 2021-11-08T23:04:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917458203-FlagStat 2021-11-08T23:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917459227-CombineGenotypingArrayVcfs-Picard 2021-11-08T23:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917460123-BaitDesigner-Picard 2021-11-08T23:07:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917462043-ValidateSamFile-Picard 2021-11-08T23:04:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917463195-FastqToSam-Picard 2021-11-08T23:07:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917464475-CollectIlluminaBasecallingMetrics-Picard 2021-11-08T23:04:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917466011-ConvertHeaderlessHadoopBamShardToBam-BETA 2021-11-08T23:04:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917467291-CollectRnaSeqMetrics-Picard 2021-11-08T23:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917468187-GatherVcfsCloud-BETA 2021-11-08T23:04:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917469339-PathSeqScoreSpark 2021-11-08T23:08:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917470491-PassesVendorQualityCheckReadFilter 2021-11-08T23:04:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917471643-AS-MappingQualityRankSumTest 2021-11-08T23:04:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917472667-ReadPosRankSumTest 2021-11-08T23:04:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917474843-BaseQuality 2021-11-08T23:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917476123-SeqIsStoredReadFilter 2021-11-08T23:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917477147-NonZeroReferenceLengthAlignmentReadFilter 2021-11-08T23:04:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917478427-PathSeqFilterSpark 2021-11-08T23:08:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917479963-FastaAlternateReferenceMaker 2021-11-08T23:08:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917481499-StructuralVariationDiscoveryPipelineSpark-BETA 2021-11-08T23:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917482651-SplitNCigarReads 2021-11-08T23:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917483675-NonZeroFragmentLengthReadFilter 2021-11-08T23:05:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917484571-DepthOfCoverage-BETA 2021-11-08T23:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917485595-PileupSpark-BETA 2021-11-08T23:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917486747-SplitVcfs-Picard 2021-11-08T23:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917488795-CNNVariantTrain-EXPERIMENTAL 2021-11-08T23:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917490459-FindBadGenomicKmersSpark-BETA 2021-11-08T23:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917491483-AnalyzeSaturationMutagenesis-BETA 2021-11-08T23:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917492635-AS-BaseQualityRankSumTest 2021-11-08T23:05:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917493531-Concordance 2021-11-08T23:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917494683-BuildBamIndex-Picard 2021-11-08T23:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917496219-NotSecondaryAlignmentReadFilter 2021-11-08T23:05:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917497371-FindMendelianViolations-Picard 2021-11-08T23:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917498651-ShiftFasta-BETA 2021-11-08T23:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917499931-IndexFeatureFile 2021-11-08T23:05:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917501467-AlleleFraction 2021-11-08T23:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917502363-ConvertSequencingArtifactToOxoG-Picard 2021-11-08T23:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917503387-OrientationBiasReadCounts 2021-11-08T23:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917504411-AssemblyComplexity 2021-11-08T23:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917505563-RenameSampleInVcf-Picard 2021-11-08T23:08:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917506459-ReadAnonymizer-EXPERIMENTAL 2021-11-08T23:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917507355-MappingQualityAvailableReadFilter 2021-11-08T23:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917508379-CreateReadCountPanelOfNormals 2021-11-08T23:05:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409917510811-CalibrateDragstrModel 2021-11-08T23:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924780827-BedToIntervalList-Picard 2021-11-08T23:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924781851-CompareDuplicatesSpark-BETA 2021-11-08T23:07:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924782747-CollectRawWgsMetrics-Picard 2021-11-08T23:07:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924783771-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2021-11-08T23:07:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924785691-MarkDuplicates-Picard 2021-11-08T23:03:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924787995-GoodCigarReadFilter 2021-11-08T23:03:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924791323-ReorderSam-Picard 2021-11-08T23:03:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924792347-PostprocessGermlineCNVCalls 2021-11-08T23:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924793883-GenotypeSummaries 2021-11-08T23:03:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924795547-AS-ReadPosRankSumTest 2021-11-08T23:03:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924798619-RevertBaseQualityScores 2021-11-08T23:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924799643-GatherTranches-BETA 2021-11-08T23:03:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924802331-PossibleDeNovo 2021-11-08T23:03:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924803227-CollectInsertSizeMetricsSpark-BETA 2021-11-08T23:07:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924805147-ApplyVQSR 2021-11-08T23:07:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924806043-PrintSVEvidence-EXPERIMENTAL 2021-11-08T23:07:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924807067-UpdateVcfSequenceDictionary-Picard 2021-11-08T23:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924808219-MappingQualityZero 2021-11-08T23:03:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924810011-CollectArraysVariantCallingMetrics-Picard 2021-11-08T23:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924811291-CollectVariantCallingMetrics-Picard 2021-11-08T23:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924812827-LiftoverVcf-Picard 2021-11-08T23:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924813723-ReadPosition 2021-11-08T23:04:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924814747-MateOnSameContigOrNoMappedMateReadFilter 2021-11-08T23:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924815771-ApplyBQSRSpark-BETA 2021-11-08T23:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924816667-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2021-11-08T23:04:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924817691-MergeVcfs-Picard 2021-11-08T23:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924818971-ExtractSVEvidenceSpark-BETA 2021-11-08T23:07:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924820123-CNNScoreVariants 2021-11-08T23:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924821531-PrintDistantMates 2021-11-08T23:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924822939-InbreedingCoeff 2021-11-08T23:04:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924823963-ReadLengthEqualsCigarLengthReadFilter 2021-11-08T23:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924827035-ReadGroupBlackListReadFilter 2021-11-08T23:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924828187-SortSam-Picard 2021-11-08T23:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924830875-AnnotateIntervals 2021-11-08T23:08:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924832795-SplitReads 2021-11-08T23:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924835739-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2021-11-08T23:08:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924837275-PlotDenoisedCopyRatios 2021-11-08T23:04:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924839067-EvaluateInfoFieldConcordance-BETA 2021-11-08T23:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924841883-SplitSamByLibrary-Picard 2021-11-08T23:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924843675-AddCommentsToBam-Picard 2021-11-08T23:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924847899-ReferenceBases 2021-11-08T23:05:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924848923-MetricsReadFilter 2021-11-08T23:05:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924850715-QualityScoreDistributionSpark-BETA 2021-11-08T23:08:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924851611-DepthPerSampleHC 2021-11-08T23:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924854683-CollectOxoGMetrics-Picard 2021-11-08T23:05:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924855707-CollectDuplicateMetrics-Picard 2021-11-08T23:05:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924856603-CountReadsSpark 2021-11-08T23:08:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924857627-CountBasesSpark 2021-11-08T23:08:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924858523-PrintReadsSpark 2021-11-08T23:08:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924859675-ASEReadCounter 2021-11-08T23:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924861211-CreateSomaticPanelOfNormals-BETA 2021-11-08T23:08:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924862491-CheckPileup 2021-11-08T23:08:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924864027-ReadLengthReadFilter 2021-11-08T23:05:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4409924864923-CleanSam-Picard 2021-11-08T23:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4410456501915-Functional-equivalence-in-DRAGEN-GATK 2024-07-08T20:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4410953761563-Introducing-DRAGMAP-the-new-genome-mapper-in-DRAGEN-GATK 2024-07-01T17:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4411716682011-Full-release-of-open-source-DRAGEN-GATK-1-0 2024-07-01T17:07:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4412955012379-Important-GATK-version-update-required-to-address-Log4j-security-vulnerability 2022-11-15T13:15:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056149403-LibraryReadFilter 2021-12-16T20:00:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056151579-MeanQualityByCycle-Picard 2021-12-16T20:05:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056153115-Pileup 2021-12-16T20:05:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056154139-WellformedReadFilter 2021-12-16T20:05:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056155419-SampleReadFilter 2021-12-16T20:00:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056156699-AnalyzeCovariates 2021-12-16T20:05:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056158235-Funcotator 2021-12-16T20:05:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056160667-AlignmentAgreesWithHeaderReadFilter 2021-12-16T20:00:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056161947-FilterVcf-Picard 2021-12-16T20:00:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056163355-VariantEval-BETA 2021-12-16T20:00:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056165659-EstimateLibraryComplexity-Picard 2021-12-16T20:00:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056167963-NotDuplicateReadFilter 2021-12-16T20:00:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056168859-BamToBfq-Picard 2021-12-16T20:00:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056174235-PrimaryLineReadFilter 2021-12-16T20:00:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056176283-CollectMultipleMetricsSpark-BETA 2021-12-16T20:05:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056177947-StrandOddsRatio 2021-12-16T20:00:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056185627-UniqueAltReadCount 2021-12-16T20:00:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056186907-MappingQuality 2021-12-16T20:00:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056194203-UpdateVCFSequenceDictionary 2021-12-16T20:05:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056195355-IlluminaBasecallsToFastq-Picard 2021-12-16T20:00:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056197915-FisherStrand 2021-12-16T20:01:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056199067-GeneExpressionEvaluation-BETA 2021-12-16T20:05:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056199963-ClusterCrosscheckMetrics-Picard 2021-12-16T20:01:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056201627-CollectSamErrorMetrics-Picard 2021-12-16T20:01:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056203803-MarkDuplicatesSpark 2021-12-16T20:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056205083-DepthPerAlleleBySample 2021-12-16T20:01:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056206107-CalculateReadGroupChecksum-Picard 2021-12-16T20:05:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056207003-CompareMetrics-Picard 2021-12-16T20:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056208283-FuncotateSegments-BETA 2021-12-16T20:06:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056209435-PathSeqBuildReferenceTaxonomy 2021-12-16T20:01:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056214299-GatherVcfs-Picard 2021-12-16T20:01:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056215579-MappedReadFilter 2021-12-16T20:01:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056217627-ExtractSequences-Picard 2021-12-16T20:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056219163-MarkDuplicatesWithMateCigar-Picard 2021-12-16T20:06:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056220187-CalculateContamination 2021-12-16T20:06:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056221339-ApplyBQSR 2021-12-16T20:06:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056222235-CpxVariantReInterpreterSpark-BETA 2021-12-16T20:06:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056223259-PathSeqBuildKmers 2021-12-16T20:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056224795-IntervalListTools-Picard 2021-12-16T20:06:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056226715-FragmentDepthPerAlleleBySample 2021-12-16T20:01:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056230555-MappingQualityRankSumTest 2021-12-16T20:01:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056232219-MappingQualityNotZeroReadFilter 2021-12-16T20:01:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056233755-HaplotypeCallerSpark-BETA 2021-12-16T20:06:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056235035-CollectJumpingLibraryMetrics-Picard 2021-12-16T20:01:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056236699-SplitSamByNumberOfReads-Picard 2021-12-16T20:06:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056238107-NonNFastaSize-Picard 2021-12-16T20:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056239643-AccumulateVariantCallingMetrics-Picard 2021-12-16T20:01:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056241051-ReadGroupReadFilter 2021-12-16T20:01:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056242203-GenomicsDBImport 2021-12-16T20:06:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056245147-PrintReads 2021-12-16T20:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056246299-BwaAndMarkDuplicatesPipelineSpark-BETA 2021-12-16T20:06:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056248219-ValidAlignmentStartReadFilter 2021-12-16T20:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056249371-ReplaceSamHeader-Picard 2021-12-16T20:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056251035-MateUnmappedAndUnmappedReadFilter 2021-12-16T20:02:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056252059-VcfToIntervalList-Picard 2021-12-16T20:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056253723-MarkIlluminaAdapters-Picard 2021-12-16T20:06:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056256795-MeanQualityByCycleSpark-BETA 2021-12-16T20:06:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056258075-CheckIlluminaDirectory-Picard 2021-12-16T20:06:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056259355-CollectTargetedPcrMetrics-Picard 2021-12-16T20:06:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056260379-CollectBaseDistributionByCycle-Picard 2021-12-16T20:02:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056263323-FeaturizedReadSets 2021-12-16T20:02:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056264731-ExtractIlluminaBarcodes-Picard 2021-12-16T20:02:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056265755-AmbiguousBaseReadFilter 2021-12-16T20:02:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056266651-BedToIntervalList-Picard 2021-12-16T20:06:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056268187-RemoveNearbyIndels 2021-12-16T20:06:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056271899-OriginalAlignment 2021-12-16T20:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056273307-CreateSequenceDictionary-Picard 2021-12-16T20:06:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056274459-VcfToAdpc-Picard 2021-12-16T20:02:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056275483-GoodCigarReadFilter 2021-12-16T20:02:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056276507-ReorderSam-Picard 2021-12-16T20:02:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056278171-NotSupplementaryAlignmentReadFilter 2021-12-16T20:02:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056279835-FilterAlignmentArtifacts-EXPERIMENTAL 2021-12-16T20:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056280731-PairedReadFilter 2021-12-16T20:02:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056281755-FifoBuffer-Picard 2021-12-16T20:02:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056283163-VariantFiltration 2021-12-16T20:07:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056284059-LikelihoodRankSumTest 2021-12-16T20:02:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056285339-RevertBaseQualityScores 2021-12-16T20:07:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056288283-ApplyVQSR 2021-12-16T20:07:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056289563-PrintSVEvidence-EXPERIMENTAL 2021-12-16T20:07:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056290459-UpdateVcfSequenceDictionary-Picard 2021-12-16T20:03:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056291611-MappingQualityZero 2021-12-16T20:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056293659-CallCopyRatioSegments 2021-12-16T20:03:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056296987-CombineGVCFs 2021-12-16T20:07:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056298907-AddOATag-Picard 2021-12-16T20:07:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056299931-ReadPosition 2021-12-16T20:03:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056301467-ApplyBQSRSpark-BETA 2021-12-16T20:07:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056304155-QualityScoreDistribution-Picard 2021-12-16T20:03:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056305307-PrintDistantMates 2021-12-16T20:07:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056306587-FlagStat 2021-12-16T20:07:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056307867-FixMateInformation-Picard 2021-12-16T20:03:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056309147-PrintVariantsSpark 2021-12-16T20:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056310683-ValidateSamFile-Picard 2021-12-16T20:03:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056311963-BpmToNormalizationManifestCsv-Picard 2021-12-16T20:07:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056313371-CollectIlluminaBasecallingMetrics-Picard 2021-12-16T20:03:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056314907-AnnotateIntervals 2021-12-16T20:07:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056319131-VariantRecalibrator 2021-12-16T20:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056321051-SplitIntervals 2021-12-16T20:08:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056322203-UnmarkDuplicates 2021-12-16T20:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056323483-StructuralVariationDiscoveryPipelineSpark-BETA 2021-12-16T20:08:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056324379-EvaluateInfoFieldConcordance-BETA 2021-12-16T20:08:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056326171-SplitVcfs-Picard 2021-12-16T20:08:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056328347-SplitSamByLibrary-Picard 2021-12-16T20:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056329755-CNNVariantTrain-EXPERIMENTAL 2021-12-16T20:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056330651-GenotypeGVCFs 2021-12-16T20:08:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056331547-TandemRepeat 2021-12-16T20:04:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056333467-AnalyzeSaturationMutagenesis-BETA 2021-12-16T20:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056334491-AS-BaseQualityRankSumTest 2021-12-16T20:04:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056338715-Concordance 2021-12-16T20:08:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056343195-NotSecondaryAlignmentReadFilter 2021-12-16T20:04:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056351003-IndexFeatureFile 2021-12-16T20:04:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056355867-MetricsReadFilter 2021-12-16T20:04:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056359195-FastaReferenceMaker 2021-12-16T20:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056360219-QualityScoreDistributionSpark-BETA 2021-12-16T20:08:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056361499-AlleleFraction 2021-12-16T20:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056364571-OrientationBiasReadCounts 2021-12-16T20:04:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056366875-CountNs 2021-12-16T20:04:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056369435-ReadAnonymizer-EXPERIMENTAL 2021-12-16T20:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056371227-CollectOxoGMetrics-Picard 2021-12-16T20:04:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056372635-CollectDuplicateMetrics-Picard 2021-12-16T20:04:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056376475-CheckPileup 2021-12-16T20:08:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4413056379547-CleanSam-Picard 2021-12-16T20:05:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072275099-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2021-12-16T20:05:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072276379-ChromosomeCounts 2021-12-16T20:00:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072277787-NonChimericOriginalAlignmentReadFilter 2021-12-16T20:00:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072281499-OverclippedReadFilter 2021-12-16T20:00:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072283035-BwaMemIndexImageCreator 2021-12-16T20:05:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072285723-RMSMappingQuality 2021-12-16T20:00:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072286747-FirstOfPairReadFilter 2021-12-16T20:00:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072292763-SecondOfPairReadFilter 2021-12-16T20:00:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072294171-AS-StrandOddsRatio 2021-12-16T20:00:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072295579-CountReads 2021-12-16T20:05:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072296731-FixVcfHeader-Picard 2021-12-16T20:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072298267-GnarlyGenotyper-BETA 2021-12-16T20:05:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072299547-PrintReadsHeader 2021-12-16T20:05:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072300443-ViewSam-Picard 2021-12-16T20:05:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072301851-LiftOverIntervalList-Picard 2021-12-16T20:00:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072303387-FilterSamReads-Picard 2021-12-16T20:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072304411-MergePedIntoVcf-Picard 2021-12-16T20:00:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072306715-CountBases 2021-12-16T20:05:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072311323-HasReadGroupReadFilter 2021-12-16T20:00:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072312475-DetermineGermlineContigPloidy 2021-12-16T20:00:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072317083-QualByDepth 2021-12-16T20:00:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072319259-NormalizeFasta-Picard 2021-12-16T20:05:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072321307-CountVariantsSpark 2021-12-16T20:00:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072328603-ClipReads 2021-12-16T20:05:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072330523-SoftClippedReadFilter 2021-12-16T20:01:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072331675-GetSampleName 2021-12-16T20:05:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072333851-SetNmMdAndUqTags-Picard 2021-12-16T20:05:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072337819-BwaSpark-BETA 2021-12-16T20:06:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072340763-CollectAlignmentSummaryMetrics-Picard 2021-12-16T20:01:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072344731-GatherBQSRReports 2021-12-16T20:01:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072347931-CollectInsertSizeMetrics-Picard 2021-12-16T20:01:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072349083-LearnReadOrientationModel 2021-12-16T20:01:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072350235-CollectReadCounts 2021-12-16T20:06:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072351515-SortSamSpark-BETA 2021-12-16T20:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072354459-ComposeSTRTableFile 2021-12-16T20:06:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072355355-MateDifferentStrandReadFilter 2021-12-16T20:06:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072356507-BaseRecalibratorSpark-BETA 2021-12-16T20:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072357659-CalculateMixingFractions 2021-12-16T20:06:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072359451-MappingQualityReadFilter 2021-12-16T20:06:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072361627-CreateBafRegressMetricsFile-Picard 2021-12-16T20:01:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072363419-CreateHadoopBamSplittingIndex-BETA 2021-12-16T20:01:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072365595-ReadsPipelineSpark-BETA 2021-12-16T20:06:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072366619-CountFalsePositives-BETA 2021-12-16T20:06:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072367771-CollectIlluminaLaneMetrics-Picard 2021-12-16T20:02:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072368923-CountBasesInReference 2021-12-16T20:06:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072370459-FragmentLength 2021-12-16T20:02:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072372507-FixMisencodedBaseQualityReads 2021-12-16T20:06:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072374299-ModelSegments 2021-12-16T20:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072375835-RevertSamSpark-BETA 2021-12-16T20:06:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072378395-CompareDuplicatesSpark-BETA 2021-12-16T20:06:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072380315-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2021-12-16T20:06:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072382107-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-12-16T20:02:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072383003-AllelePseudoDepth 2021-12-16T20:02:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072384155-PostprocessGermlineCNVCalls 2021-12-16T20:07:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072386075-GenotypeSummaries 2021-12-16T20:02:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072386971-FlagStatSpark 2021-12-16T20:07:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072389787-GetPileupSummaries 2021-12-16T20:07:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072391835-GatherTranches-BETA 2021-12-16T20:02:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072392731-DownsampleSam-Picard 2021-12-16T20:07:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072394011-ClippingRankSumTest 2021-12-16T20:02:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072395291-CompareSAMs-Picard 2021-12-16T20:07:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072396315-BQSRPipelineSpark-BETA 2021-12-16T20:07:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072400539-PossibleDeNovo 2021-12-16T20:03:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072401435-CollectInsertSizeMetricsSpark-BETA 2021-12-16T20:07:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072402459-BaseQualityRankSumTest 2021-12-16T20:03:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072403483-IntervalListToBed-Picard 2021-12-16T20:03:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072404635-GermlineCNVCaller 2021-12-16T20:03:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072408475-AS-InbreedingCoeff 2021-12-16T20:03:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072410523-BamIndexStats-Picard 2021-12-16T20:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072413851-CollectVariantCallingMetrics-Picard 2021-12-16T20:03:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072417307-LiftoverVcf-Picard 2021-12-16T20:07:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072418715-MateOnSameContigOrNoMappedMateReadFilter 2021-12-16T20:07:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072419611-ReadStrandFilter 2021-12-16T20:03:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072421403-CalculateGenotypePosteriors 2021-12-16T20:07:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072423323-CollectAllelicCounts 2021-12-16T20:07:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072424347-CNNScoreVariants 2021-12-16T20:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072425371-MethylationTypeCaller-EXPERIMENTAL 2021-12-16T20:07:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072426523-PreprocessIntervals 2021-12-16T20:07:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072428059-CombineGenotypingArrayVcfs-Picard 2021-12-16T20:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072429979-ReadLengthEqualsCigarLengthReadFilter 2021-12-16T20:07:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072431131-SortVcf-Picard 2021-12-16T20:07:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072432795-FastqToSam-Picard 2021-12-16T20:07:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072433691-ReadGroupBlackListReadFilter 2021-12-16T20:03:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072434587-SamToFastq-Picard 2021-12-16T20:07:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072436123-FuncotatorDataSourceDownloader 2021-12-16T20:03:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072437403-ConvertHeaderlessHadoopBamShardToBam-BETA 2021-12-16T20:03:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072438427-GatherVcfsCloud-BETA 2021-12-16T20:03:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072439579-PathSeqScoreSpark 2021-12-16T20:08:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072440603-RevertSam-Picard 2021-12-16T20:08:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072441627-AS-MappingQualityRankSumTest 2021-12-16T20:04:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072442907-ReadPosRankSumTest 2021-12-16T20:04:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072443803-BaseQuality 2021-12-16T20:04:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072445211-SeqIsStoredReadFilter 2021-12-16T20:04:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072446107-IntervalOverlapReadFilter 2021-12-16T20:04:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072447515-CollectBaseDistributionByCycleSpark-BETA 2021-12-16T20:08:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072448667-PathSeqFilterSpark 2021-12-16T20:08:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072451611-DepthOfCoverage-BETA 2021-12-16T20:08:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072452507-PileupSpark-BETA 2021-12-16T20:08:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072456219-FindBadGenomicKmersSpark-BETA 2021-12-16T20:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072461083-AS-QualByDepth 2021-12-16T20:08:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072464539-FindMendelianViolations-Picard 2021-12-16T20:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072467227-ValidAlignmentEndReadFilter 2021-12-16T20:08:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072470171-DepthPerSampleHC 2021-12-16T20:04:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072472091-ConvertSequencingArtifactToOxoG-Picard 2021-12-16T20:04:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072474523-AssemblyComplexity 2021-12-16T20:04:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072476443-RenameSampleInVcf-Picard 2021-12-16T20:08:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072480155-MappingQualityAvailableReadFilter 2021-12-16T20:04:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072481563-CreateReadCountPanelOfNormals 2021-12-16T20:04:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072486939-CountBasesSpark 2021-12-16T20:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072488987-PrintReadsSpark 2021-12-16T20:08:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072490779-CalibrateDragstrModel 2021-12-16T20:08:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072491931-FilterVariantTranches 2021-12-16T20:08:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072493595-CreateSomaticPanelOfNormals-BETA 2021-12-16T20:08:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072496027-GtcToVcf-Picard 2021-12-16T20:05:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4413072497947-ReadLengthReadFilter 2021-12-16T20:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079115291-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2021-12-16T20:00:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079119003-CollectHiSeqXPfFailMetrics-Picard 2021-12-16T20:00:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079120027-GenotypeConcordance-Picard 2021-12-16T20:05:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079121051-NotProperlyPairedReadFilter 2021-12-16T20:00:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079123867-CollectQualityYieldMetrics-Picard 2021-12-16T20:00:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079125147-PathSeqPipelineSpark 2021-12-16T20:05:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079126555-CalcMetadataSpark-BETA 2021-12-16T20:05:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079128603-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2021-12-16T20:05:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079130907-CollectHsMetrics-Picard 2021-12-16T20:05:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079132571-AnnotateVcfWithExpectedAlleleFraction 2021-12-16T20:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079133851-CountVariants 2021-12-16T20:05:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079135131-AllowAllReadsReadFilter 2021-12-16T20:00:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079137691-VariantAnnotator 2021-12-16T20:05:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079147803--Tool-Documentation-Index 2021-12-16T20:05:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079149979-CheckFingerprint-Picard 2021-12-16T20:00:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079153819-FindBreakpointEvidenceSpark-BETA 2021-12-16T20:05:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079160091-VariantsToTable 2021-12-16T20:05:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079161243-AS-RMSMappingQuality 2021-12-16T20:00:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079162395-CNNVariantWriteTensors-EXPERIMENTAL 2021-12-16T20:05:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079169435-SamFormatConverter-Picard 2021-12-16T20:00:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079174939-GatherBamFiles-Picard 2021-12-16T20:01:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079176091-CalculateFingerprintMetrics-Picard 2021-12-16T20:01:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079178011-AS-FisherStrand 2021-12-16T20:01:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079179035-CompareBaseQualities 2021-12-16T20:01:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079184027-AnnotateVcfWithBamDepth 2021-12-16T20:06:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079185051-CollectSequencingArtifactMetrics-Picard 2021-12-16T20:01:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079195035-MakeSitesOnlyVcf-Picard 2021-12-16T20:06:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079197211-StrandBiasBySample 2021-12-16T20:01:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079200667-LeftAlignIndels 2021-12-16T20:06:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079201563-FilterIntervals 2021-12-16T20:01:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079204891-FilterMutectCalls 2021-12-16T20:06:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079206811-SelectVariants 2021-12-16T20:06:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079208731-IlluminaBasecallsToSam-Picard 2021-12-16T20:01:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079211803-CollectQualityYieldMetricsSpark-BETA 2021-12-16T20:06:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079213083-PlatformUnitReadFilter 2021-12-16T20:01:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079216155-MateDistantReadFilter 2021-12-16T20:06:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079217179-HaplotypeCaller 2021-12-16T20:06:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079219739-SetNmAndUqTags-Picard 2021-12-16T20:06:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079220763-PathSeqBwaSpark 2021-12-16T20:06:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079222171-SampleList 2021-12-16T20:02:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079223067-MatchingBasesAndQualsReadFilter 2021-12-16T20:02:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079223963-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2021-12-16T20:06:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079226139-ReblockGVCF 2021-12-16T20:06:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079227291-MergeBamAlignment-Picard 2021-12-16T20:02:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079229723-LeftAlignAndTrimVariants 2021-12-16T20:06:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079232923-CollectRawWgsMetrics-Picard 2021-12-16T20:06:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079236123-MarkDuplicates-Picard 2021-12-16T20:02:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079237787-PositionBasedDownsampleSam-Picard 2021-12-16T20:02:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079240731-CollectWgsMetrics-Picard 2021-12-16T20:02:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079242267-AS-ReadPosRankSumTest 2021-12-16T20:02:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079244059-ExcessHet 2021-12-16T20:02:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079245467-BaseRecalibrator 2021-12-16T20:07:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079247387-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2021-12-16T20:07:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079248667-DenoiseReadCounts 2021-12-16T20:03:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079250075-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2021-12-16T20:07:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079256475-ReadNameReadFilter 2021-12-16T20:03:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079260059-ScatterIntervalsByNs-Picard 2021-12-16T20:07:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079261723-PlatformReadFilter 2021-12-16T20:03:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079262875-Mutect2 2021-12-16T20:07:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079263899-CollectArraysVariantCallingMetrics-Picard 2021-12-16T20:07:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079264923-VcfFormatConverter-Picard 2021-12-16T20:07:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079266075-AddOrReplaceReadGroups-Picard 2021-12-16T20:03:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079267483-PlotModeledSegments 2021-12-16T20:03:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079269275-LocalAssembler-BETA 2021-12-16T20:07:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079271067-CollectGcBiasMetrics-Picard 2021-12-16T20:03:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079273243-Coverage 2021-12-16T20:03:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079274395-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2021-12-16T20:03:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079275419-MergeVcfs-Picard 2021-12-16T20:07:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079276571-CollectMultipleMetrics-Picard 2021-12-16T20:07:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079277851-ValidateVariants 2021-12-16T20:07:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079279259-ExtractSVEvidenceSpark-BETA 2021-12-16T20:07:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079281051-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2021-12-16T20:03:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079283867-BaitDesigner-Picard 2021-12-16T20:07:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079284763-InbreedingCoeff 2021-12-16T20:03:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079287195-SortSam-Picard 2021-12-16T20:07:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079289371-MergeSamFiles-Picard 2021-12-16T20:07:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079290267-CollectRnaSeqMetrics-Picard 2021-12-16T20:03:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079291931-PassesVendorQualityCheckReadFilter 2021-12-16T20:04:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079292827-SplitReads 2021-12-16T20:08:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079295131-NonZeroReferenceLengthAlignmentReadFilter 2021-12-16T20:04:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079297947-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2021-12-16T20:08:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079299099-PlotDenoisedCopyRatios 2021-12-16T20:04:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079299995-FastaAlternateReferenceMaker 2021-12-16T20:08:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079301787-SplitNCigarReads 2021-12-16T20:08:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079302683-NonZeroFragmentLengthReadFilter 2021-12-16T20:04:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079304219-ProperlyPairedReadFilter 2021-12-16T20:04:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079305115-CigarContainsNoNOperator 2021-12-16T20:04:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079306523-FilterFuncotations-EXPERIMENTAL 2021-12-16T20:08:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079307675-CrosscheckFingerprints-Picard 2021-12-16T20:08:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079309851-AddCommentsToBam-Picard 2021-12-16T20:08:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079318299-FragmentLengthReadFilter 2021-12-16T20:04:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079319707-BuildBamIndex-Picard 2021-12-16T20:08:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079320987-CollectRrbsMetrics-Picard 2021-12-16T20:04:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079325595-ShiftFasta-BETA 2021-12-16T20:08:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079327259-ReferenceBases 2021-12-16T20:04:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079345051-CountReadsSpark 2021-12-16T20:08:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079346331-ASEReadCounter 2021-12-16T20:08:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4413079352731-CheckTerminatorBlock-Picard 2021-12-16T20:05:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586716699-NonChimericOriginalAlignmentReadFilter 2022-01-05T00:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586717851-CollectHiSeqXPfFailMetrics-Picard 2022-01-05T00:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586718747-GenotypeConcordance-Picard 2022-01-05T00:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586719771-Pileup 2022-01-05T00:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586721051-WellformedReadFilter 2022-01-05T00:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586723611-CollectQualityYieldMetrics-Picard 2022-01-05T00:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586726683-AS-StrandOddsRatio 2022-01-05T00:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586727579-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2022-01-05T00:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586728603-CountReads 2022-01-05T00:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586729499-FixVcfHeader-Picard 2022-01-05T00:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586731035-CountVariants 2022-01-05T00:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586731931-AllowAllReadsReadFilter 2022-01-05T00:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586733211-NotDuplicateReadFilter 2022-01-05T00:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586734107-BamToBfq-Picard 2022-01-05T00:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586735259-MergePedIntoVcf-Picard 2022-01-05T00:53:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586736539-CollectMultipleMetricsSpark-BETA 2022-01-05T00:57:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586737819-CountBases 2022-01-05T00:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586739611-DetermineGermlineContigPloidy 2024-06-27T11:27:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586740763-CNNVariantWriteTensors-EXPERIMENTAL 2022-01-05T00:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586742171-IlluminaBasecallsToFastq-Picard 2022-01-05T00:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586743195-SamFormatConverter-Picard 2022-01-05T00:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586744987-DepthPerAlleleBySample 2022-01-05T00:54:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586746395-CompareMetrics-Picard 2022-01-05T00:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586747419-FuncotateSegments-BETA 2022-01-05T00:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586748571-CalculateFingerprintMetrics-Picard 2022-01-05T00:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586750235-CollectSequencingArtifactMetrics-Picard 2022-01-05T00:54:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586751771-CalculateContamination 2022-01-05T00:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586753307-StrandBiasBySample 2022-01-05T00:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586754715-LeftAlignIndels 2022-01-05T00:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586755995-ComposeSTRTableFile 2022-01-05T00:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586757275-MateDifferentStrandReadFilter 2022-01-05T00:58:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586758299-FilterMutectCalls 2022-01-05T00:58:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586759323-BaseRecalibratorSpark-BETA 2022-01-05T00:58:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586760219-CalculateMixingFractions 2022-01-05T00:58:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586761499-IlluminaBasecallsToSam-Picard 2022-01-05T00:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586762651-GenomicsDBImport 2022-01-05T00:58:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586764571-MateDistantReadFilter 2022-01-05T00:58:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586765723-HaplotypeCaller 2022-03-11T17:34:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586767003-ReadsPipelineSpark-BETA 2022-01-05T00:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586768155-CountFalsePositives-BETA 2022-01-05T00:58:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586769307-CollectIlluminaLaneMetrics-Picard 2022-01-05T00:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586771227-PathSeqBwaSpark 2022-01-05T00:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586772379-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2022-01-05T00:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586773787-CheckIlluminaDirectory-Picard 2022-01-05T00:58:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586775963-RevertSamSpark-BETA 2022-01-05T00:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586777243-BedToIntervalList-Picard 2022-01-05T00:58:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586780059-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2022-01-05T00:58:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586781083-VcfToAdpc-Picard 2022-01-05T00:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586782107-PositionBasedDownsampleSam-Picard 2022-01-05T00:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586783771-FilterAlignmentArtifacts-EXPERIMENTAL 2022-01-05T00:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586785947-GetPileupSummaries 2022-01-05T00:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586786843-FifoBuffer-Picard 2022-01-05T00:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586789019-DownsampleSam-Picard 2022-01-05T00:58:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586790555-CompareSAMs-Picard 2022-01-05T00:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586791963-BQSRPipelineSpark-BETA 2022-01-05T00:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586793371-PossibleDeNovo 2022-01-05T00:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586794523-DenoiseReadCounts 2022-01-05T00:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586795419-BaseQualityRankSumTest 2022-01-05T00:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586797467-GermlineCNVCaller 2022-01-05T00:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586798619-UpdateVcfSequenceDictionary-Picard 2022-01-05T00:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586800155-MappingQualityZero 2022-01-05T00:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586801179-ScatterIntervalsByNs-Picard 2022-01-05T00:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586802459-AS-InbreedingCoeff 2022-01-05T00:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586803739-LocalAssembler-BETA 2022-01-05T00:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586805787-ApplyBQSRSpark-BETA 2022-01-05T00:59:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586807195-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2022-01-05T00:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586808859-CollectAllelicCounts 2022-01-05T00:59:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586811803-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2022-01-05T00:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586814107-MethylationTypeCaller-EXPERIMENTAL 2022-01-05T00:59:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586816027-QualityScoreDistribution-Picard 2022-01-05T00:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586817051-FlagStat 2022-01-05T00:59:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586818459-BaitDesigner-Picard 2022-01-05T00:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586819483-ReadLengthEqualsCigarLengthReadFilter 2022-01-05T00:59:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586820379-FixMateInformation-Picard 2022-01-05T00:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586821915-SortVcf-Picard 2022-01-05T00:59:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586823963-BpmToNormalizationManifestCsv-Picard 2022-01-05T00:59:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586826523-SortSam-Picard 2022-01-05T00:59:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586827419-CollectIlluminaBasecallingMetrics-Picard 2022-01-05T00:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586829467-PassesVendorQualityCheckReadFilter 2022-01-05T00:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586830491-AS-MappingQualityRankSumTest 2022-01-05T00:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586832283-CollectBaseDistributionByCycleSpark-BETA 2022-01-05T00:59:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586833179-VariantRecalibrator 2022-01-05T00:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586834459-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2022-01-05T00:59:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586835355-PlotDenoisedCopyRatios 2022-01-05T00:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586837147-UnmarkDuplicates 2022-01-05T00:59:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586839451-StructuralVariationDiscoveryPipelineSpark-BETA 2022-01-05T00:59:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586840475-EvaluateInfoFieldConcordance-BETA 2022-01-05T00:59:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586842523-DepthOfCoverage-BETA 2022-01-05T00:59:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586843675-ProperlyPairedReadFilter 2022-01-05T00:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586844827-FilterFuncotations-EXPERIMENTAL 2022-01-05T00:59:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586846235-CNNVariantTrain-EXPERIMENTAL 2022-01-05T00:59:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586847899-AddCommentsToBam-Picard 2022-01-05T00:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586848795-AS-QualByDepth 2022-01-05T00:59:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586849819-Concordance 2022-01-05T00:59:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586850971-FindMendelianViolations-Picard 2022-01-05T00:59:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586851867-ShiftFasta-BETA 2022-01-05T00:59:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586853147-IndexFeatureFile 2022-01-05T00:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586854043-MetricsReadFilter 2022-01-05T00:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586856091-AlleleFraction 2022-01-05T00:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586856987-ConvertSequencingArtifactToOxoG-Picard 2022-01-05T00:57:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586859419-ReadAnonymizer-EXPERIMENTAL 2022-01-05T00:59:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586860699-MappingQualityAvailableReadFilter 2022-01-05T00:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586861723-CollectDuplicateMetrics-Picard 2022-01-05T00:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586863003-ASEReadCounter 2022-01-05T01:00:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586864411-CheckPileup 2022-01-05T01:00:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4414586865435-ReadLengthReadFilter 2022-01-05T00:57:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594301339-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2022-01-05T00:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594302491-ChromosomeCounts 2022-01-05T00:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594303387-LibraryReadFilter 2022-01-05T00:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594304283-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2022-01-05T00:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594306203-NotProperlyPairedReadFilter 2022-01-05T00:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594307611-Funcotator 2022-01-05T00:57:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594308763-PathSeqPipelineSpark 2022-01-05T00:57:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594311835-SecondOfPairReadFilter 2022-01-05T00:53:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594313243-VariantEval-BETA 2022-01-05T00:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594315931-LiftOverIntervalList-Picard 2022-01-05T00:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594316955-VariantAnnotator 2022-01-05T00:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594317979-FilterSamReads-Picard 2022-01-05T00:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594319131-PrimaryLineReadFilter 2022-01-05T00:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594320155-StrandOddsRatio 2022-01-05T00:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594321179-HasReadGroupReadFilter 2022-01-05T00:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594322203-FindBreakpointEvidenceSpark-BETA 2022-01-05T00:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594323227-UniqueAltReadCount 2022-01-05T00:53:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594324251-MappingQuality 2022-01-05T00:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594325275-NormalizeFasta-Picard 2022-01-05T00:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594326299-CountVariantsSpark 2022-01-05T00:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594327195-UpdateVCFSequenceDictionary 2022-01-05T00:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594328347-ClipReads 2022-01-05T00:57:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594330011-MarkDuplicatesSpark 2022-01-05T00:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594331035-CalculateReadGroupChecksum-Picard 2022-01-05T00:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594332187-PathSeqBuildReferenceTaxonomy 2022-01-05T00:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594333467-AS-FisherStrand 2022-01-05T00:54:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594334363-BwaSpark-BETA 2022-01-05T00:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594335387-AnnotateVcfWithBamDepth 2022-01-05T00:58:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594336539-ExtractSequences-Picard 2022-01-05T00:58:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594337563-MarkDuplicatesWithMateCigar-Picard 2022-01-05T00:58:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594338459-GatherBQSRReports 2022-01-05T00:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594339611-ApplyBQSR 2022-01-05T00:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594340507-CpxVariantReInterpreterSpark-BETA 2022-01-05T00:58:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594341403-PathSeqBuildKmers 2022-01-05T00:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594342427-MakeSitesOnlyVcf-Picard 2022-01-05T00:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594343323-CollectInsertSizeMetrics-Picard 2022-01-05T00:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594344603-CollectReadCounts 2022-01-05T00:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594345627-FilterIntervals 2022-01-05T00:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594346523-MappingQualityRankSumTest 2022-01-05T00:54:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594347675-MappingQualityNotZeroReadFilter 2022-01-05T00:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594348955-NonNFastaSize-Picard 2022-01-05T00:58:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594350619-SelectVariants 2022-01-05T00:58:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594351515-AccumulateVariantCallingMetrics-Picard 2022-01-05T00:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594352667-ReadGroupReadFilter 2022-01-05T00:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594353691-MappingQualityReadFilter 2022-01-05T00:58:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594355099-CreateBafRegressMetricsFile-Picard 2022-01-05T00:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594356251-BwaAndMarkDuplicatesPipelineSpark-BETA 2022-01-05T00:58:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594358299-VcfToIntervalList-Picard 2022-01-05T00:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594359195-SetNmAndUqTags-Picard 2022-01-05T00:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594360603-SampleList 2022-01-05T00:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594361499-MatchingBasesAndQualsReadFilter 2022-01-05T00:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594362523-MeanQualityByCycleSpark-BETA 2022-01-05T00:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594363547-CollectTargetedPcrMetrics-Picard 2022-01-05T00:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594364443-CollectBaseDistributionByCycle-Picard 2022-01-05T00:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594365467-ReblockGVCF 2022-02-16T02:45:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594366363-MergeBamAlignment-Picard 2023-04-25T11:51:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594367259-FixMisencodedBaseQualityReads 2022-01-05T00:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594368667-LeftAlignAndTrimVariants 2022-01-05T00:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594369691-FeaturizedReadSets 2022-01-05T00:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594371099-RemoveNearbyIndels 2022-01-05T00:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594373659-CompareDuplicatesSpark-BETA 2022-01-05T00:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594375451-GoodCigarReadFilter 2022-01-05T00:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594376347-AllelePseudoDepth 2022-01-05T00:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594377499-PostprocessGermlineCNVCalls 2022-01-05T00:58:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594378523-NotSupplementaryAlignmentReadFilter 2022-01-05T00:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594379547-GenotypeSummaries 2022-01-05T00:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594380443-FlagStatSpark 2022-01-05T00:58:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594381723-PairedReadFilter 2022-01-05T00:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594383643-VariantFiltration 2022-01-05T00:58:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594384539-LikelihoodRankSumTest 2022-01-05T00:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594385563-BaseRecalibrator 2022-01-05T00:58:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594387483-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-01-05T00:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594389659-IntervalListToBed-Picard 2022-01-05T00:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594392347-Mutect2 2022-01-05T00:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594393243-CollectArraysVariantCallingMetrics-Picard 2022-01-05T00:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594394523-PlotModeledSegments 2022-01-05T00:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594396187-MateOnSameContigOrNoMappedMateReadFilter 2022-01-05T00:59:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594397083-Coverage 2022-01-05T00:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594398107-ReadStrandFilter 2022-01-05T00:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594402459-CollectMultipleMetrics-Picard 2022-01-05T00:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594404891-CNNScoreVariants 2022-01-05T00:59:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594407195-PreprocessIntervals 2022-01-05T00:59:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594408347-PrintDistantMates 2022-01-05T00:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594409755-InbreedingCoeff 2022-01-05T00:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594411163-SamToFastq-Picard 2022-01-05T00:59:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594412187-FuncotatorDataSourceDownloader 2022-01-05T00:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594413083-MergeSamFiles-Picard 2022-01-05T00:59:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594414107-CollectRnaSeqMetrics-Picard 2022-01-05T00:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594415003-GatherVcfsCloud-BETA 2022-01-05T00:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594415899-AnnotateIntervals 2022-01-05T00:59:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594416923-RevertSam-Picard 2022-01-05T00:59:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594417947-SplitReads 2022-01-05T00:59:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594418971-BaseQuality 2022-01-05T00:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594419867-SeqIsStoredReadFilter 2022-01-05T00:56:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594421019-IntervalOverlapReadFilter 2022-01-05T00:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594422043-NonZeroReferenceLengthAlignmentReadFilter 2022-01-05T00:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594423451-FastaAlternateReferenceMaker 2022-01-05T00:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594425627-NonZeroFragmentLengthReadFilter 2022-01-05T00:56:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594426651-PileupSpark-BETA 2022-01-05T00:59:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594428699-SplitSamByLibrary-Picard 2022-01-05T00:59:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594429595-CrosscheckFingerprints-Picard 2022-01-05T00:59:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594430619-GenotypeGVCFs 2022-01-05T00:59:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594431515-TandemRepeat 2022-01-05T00:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594432795-FindBadGenomicKmersSpark-BETA 2022-01-05T00:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594433691-AnalyzeSaturationMutagenesis-BETA 2022-01-05T00:59:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594434715-AS-BaseQualityRankSumTest 2022-01-05T00:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594435995-FragmentLengthReadFilter 2022-01-05T00:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594436891-BuildBamIndex-Picard 2022-01-05T00:59:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594437915-NotSecondaryAlignmentReadFilter 2022-01-05T00:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594439451-FastaReferenceMaker 2022-01-05T00:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594440347-QualityScoreDistributionSpark-BETA 2022-01-05T00:59:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594441371-DepthPerSampleHC 2022-01-05T00:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594442651-OrientationBiasReadCounts 2022-01-05T00:57:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594445467-PrintReadsSpark 2022-01-05T01:00:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594448795-CheckTerminatorBlock-Picard 2022-01-05T00:57:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4414594449691-CleanSam-Picard 2022-01-05T00:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602331163-MeanQualityByCycle-Picard 2022-01-05T00:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602332315-OverclippedReadFilter 2022-01-05T00:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602336411-BwaMemIndexImageCreator 2022-01-05T00:57:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602338331-SampleReadFilter 2022-01-05T00:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602339227-AnalyzeCovariates 2022-01-05T00:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602340251-RMSMappingQuality 2022-01-05T00:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602341147-FirstOfPairReadFilter 2022-01-05T00:53:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602342811-CalcMetadataSpark-BETA 2022-01-05T00:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602343835-AlignmentAgreesWithHeaderReadFilter 2022-01-05T00:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602344987-FilterVcf-Picard 2022-01-05T00:53:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602346651-CollectHsMetrics-Picard 2022-01-05T00:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602347675-GnarlyGenotyper-BETA 2022-01-05T00:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602348571-EstimateLibraryComplexity-Picard 2022-01-05T00:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602349467-PrintReadsHeader 2022-01-05T00:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602350491-ViewSam-Picard 2022-01-05T00:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602351387-AnnotateVcfWithExpectedAlleleFraction 2022-01-05T00:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602353947--Tool-Documentation-Index 2022-01-05T00:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602355099-CheckFingerprint-Picard 2022-01-05T00:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602356379-QualByDepth 2022-01-05T00:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602357275-VariantsToTable 2022-01-05T00:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602358299-AS-RMSMappingQuality 2022-01-05T00:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602359579-FisherStrand 2022-01-05T00:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602360475-GeneExpressionEvaluation-BETA 2022-01-05T00:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602361371-ClusterCrosscheckMetrics-Picard 2022-01-05T00:54:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602362523-CollectSamErrorMetrics-Picard 2022-01-05T00:54:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602363419-SoftClippedReadFilter 2022-01-05T00:54:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602364699-GetSampleName 2022-01-05T00:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602365851-SetNmMdAndUqTags-Picard 2022-01-05T00:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602367003-GatherBamFiles-Picard 2022-01-05T00:54:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602368411-CompareBaseQualities 2022-01-05T00:54:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602369435-CollectAlignmentSummaryMetrics-Picard 2022-01-05T00:54:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602370843-GatherVcfs-Picard 2022-01-05T00:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602371739-MappedReadFilter 2022-01-05T00:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602373275-IntervalListTools-Picard 2022-01-05T00:58:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602374427-FragmentDepthPerAlleleBySample 2022-01-05T00:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602375451-LearnReadOrientationModel 2022-01-05T00:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602376347-SortSamSpark-BETA 2022-01-05T00:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602377627-HaplotypeCallerSpark-BETA 2022-01-05T00:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602378523-CollectJumpingLibraryMetrics-Picard 2022-01-05T00:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602379547-SplitSamByNumberOfReads-Picard 2022-01-05T00:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602381211-CollectQualityYieldMetricsSpark-BETA 2022-01-05T00:58:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602382235-PlatformUnitReadFilter 2022-01-05T00:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602383643-CreateHadoopBamSplittingIndex-BETA 2022-01-05T00:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602384539-PrintReads 2022-01-05T00:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602386075-ValidAlignmentStartReadFilter 2022-01-05T00:58:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602386971-ReplaceSamHeader-Picard 2022-01-05T00:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602388123-MateUnmappedAndUnmappedReadFilter 2022-01-05T00:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602389147-CountBasesInReference 2022-01-05T00:58:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602390299-MarkIlluminaAdapters-Picard 2022-01-05T00:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602392091-FragmentLength 2022-01-05T00:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602393243-ModelSegments 2022-01-05T00:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602394523-ExtractIlluminaBarcodes-Picard 2022-01-05T00:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602395547-AmbiguousBaseReadFilter 2022-01-05T00:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602396571-CollectRawWgsMetrics-Picard 2022-01-05T00:58:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602397851-OriginalAlignment 2022-01-05T00:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602398747-MarkDuplicates-Picard 2022-01-05T00:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602399643-CreateSequenceDictionary-Picard 2022-01-05T00:58:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602400795-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-01-05T00:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602401947-ReorderSam-Picard 2022-01-05T00:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602403355-CollectWgsMetrics-Picard 2022-01-05T00:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602404379-AS-ReadPosRankSumTest 2022-01-05T00:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602405531-ExcessHet 2022-01-05T00:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602406683-RevertBaseQualityScores 2022-01-05T00:58:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602407707-GatherTranches-BETA 2022-01-05T00:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602408603-ClippingRankSumTest 2022-01-05T00:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602410011-CollectInsertSizeMetricsSpark-BETA 2022-01-05T00:58:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602411419-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2022-01-05T00:58:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602412827-ApplyVQSR 2022-01-05T00:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602413979-PrintSVEvidence-EXPERIMENTAL 2022-01-05T00:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602415131-ReadNameReadFilter 2022-01-05T00:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602416283-CallCopyRatioSegments 2022-01-05T00:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602417435-PlatformReadFilter 2022-01-05T00:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602418331-BamIndexStats-Picard 2022-01-05T00:59:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602419355-VcfFormatConverter-Picard 2022-01-05T00:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602420251-AddOrReplaceReadGroups-Picard 2022-01-05T00:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602421403-CollectVariantCallingMetrics-Picard 2022-01-05T00:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602422427-CombineGVCFs 2022-01-05T00:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602423451-CollectGcBiasMetrics-Picard 2022-01-05T00:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602424603-LiftoverVcf-Picard 2022-01-05T00:59:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602425755-AddOATag-Picard 2022-01-05T00:59:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602426651-ReadPosition 2022-01-05T00:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602428187-CalculateGenotypePosteriors 2022-01-05T00:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602429211-MergeVcfs-Picard 2022-01-05T00:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602430363-ValidateVariants 2022-01-05T00:59:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602431259-ExtractSVEvidenceSpark-BETA 2022-01-05T00:59:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602433691-CombineGenotypingArrayVcfs-Picard 2022-01-05T00:59:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602435483-PrintVariantsSpark 2022-01-05T00:59:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602437019-ValidateSamFile-Picard 2022-01-05T00:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602438171-FastqToSam-Picard 2022-01-05T00:59:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602439195-ReadGroupBlackListReadFilter 2022-01-05T00:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602440475-ConvertHeaderlessHadoopBamShardToBam-BETA 2022-01-05T00:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602441883-PathSeqScoreSpark 2022-01-05T00:59:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602443035-ReadPosRankSumTest 2022-01-05T00:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602447771-PathSeqFilterSpark 2022-01-05T00:59:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602449435-SplitIntervals 2022-01-05T00:59:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602451867-SplitNCigarReads 2022-01-05T00:59:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602453659-CigarContainsNoNOperator 2022-01-05T00:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602454683-SplitVcfs-Picard 2022-01-05T00:59:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602456219-CollectRrbsMetrics-Picard 2022-01-05T00:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602457499-ReferenceBases 2022-01-05T00:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602458651-ValidAlignmentEndReadFilter 2022-01-05T00:59:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602460059-AssemblyComplexity 2022-01-05T00:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602461467-CountNs 2022-01-05T00:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602462491-RenameSampleInVcf-Picard 2022-01-05T00:59:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602463771-CollectOxoGMetrics-Picard 2022-01-05T00:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602464667-CreateReadCountPanelOfNormals 2022-01-05T00:57:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602465819-CountReadsSpark 2022-01-05T00:59:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602466715-CountBasesSpark 2022-01-05T00:59:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602469531-CalibrateDragstrModel 2022-01-05T01:00:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602470555-FilterVariantTranches 2022-01-05T01:00:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602471451-CreateSomaticPanelOfNormals-BETA 2022-01-05T01:00:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4414602472475-GtcToVcf-Picard 2022-01-05T00:57:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4414910284187--DRAGEN-GATK-Webinar-Dec-2-2021 2024-07-08T20:09:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051356955-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2022-02-07T16:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051359259-CollectHiSeqXPfFailMetrics-Picard 2022-02-07T16:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051360155-GenotypeConcordance-Picard 2022-02-07T16:23:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051361435-Pileup 2022-02-07T16:23:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051363099-BwaMemIndexImageCreator 2022-02-07T16:23:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051364123-NotProperlyPairedReadFilter 2022-02-07T16:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051365275-ExcessiveEndClippedReadFilter 2022-02-07T16:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051366811-AnalyzeCovariates 2022-02-07T16:23:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051369243-PathSeqPipelineSpark 2022-04-06T08:06:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051370395-AlignmentAgreesWithHeaderReadFilter 2022-02-07T16:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051374619-AS-StrandOddsRatio 2022-02-07T16:20:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051376155-VariantEval-BETA 2022-02-07T16:20:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051377819-CollectHsMetrics-Picard 2022-02-07T16:23:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051381659-GnarlyGenotyper-BETA 2022-02-07T16:23:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051382683-PrintReadsHeader 2022-02-07T16:23:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051383707-ViewSam-Picard 2022-02-07T16:23:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051384603-AnnotateVcfWithExpectedAlleleFraction 2022-02-07T16:23:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051385883-CountVariants 2022-02-07T16:23:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051387163-AllowAllReadsReadFilter 2022-02-07T16:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051388315-BamToBfq-Picard 2022-02-07T16:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051390747-FilterSamReads-Picard 2022-02-07T16:23:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051392027-PrimaryLineReadFilter 2022-02-07T16:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051394587--Tool-Documentation-Index 2022-02-07T16:23:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051395483-CheckFingerprint-Picard 2022-02-07T16:20:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051396891-FindBreakpointEvidenceSpark-BETA 2022-02-07T16:23:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051404955-ClusterCrosscheckMetrics-Picard 2022-02-07T16:20:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051407643-GatherBamFiles-Picard 2022-02-07T16:20:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051408795-CalculateFingerprintMetrics-Picard 2022-02-07T16:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051410075-AS-FisherStrand 2022-02-07T16:20:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051412891-CompareBaseQualities 2022-02-07T16:20:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051414171-GatherVcfs-Picard 2022-02-07T16:20:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051415195-MappedReadFilter 2022-02-07T16:20:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051416859-PathSeqBuildKmers 2022-02-07T16:24:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051418395-IntervalListTools-Picard 2022-02-07T16:24:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051421211-MateDifferentStrandReadFilter 2022-02-07T16:24:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051422363-BaseRecalibratorSpark-BETA 2022-02-07T16:24:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051427867-SVCluster-BETA 2022-02-07T16:24:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051429531-GenomicsDBImport 2022-02-07T16:24:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051430939-PrintReads 2022-02-07T16:24:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051431835-BwaAndMarkDuplicatesPipelineSpark-BETA 2022-02-07T16:24:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051433243-ReadsPipelineSpark-BETA 2022-02-07T16:24:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051435035-CollectIlluminaLaneMetrics-Picard 2022-02-07T16:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051435931-CountBasesInReference 2022-02-07T16:24:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051439771-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2022-02-07T16:24:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051440923-FragmentLength 2022-02-07T16:21:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051445275-CheckIlluminaDirectory-Picard 2022-02-07T16:24:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051446811-ReblockGVCF 2022-02-07T16:24:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051452571-LeftAlignAndTrimVariants 2022-02-07T16:24:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051453851-FeaturizedReadSets 2022-02-07T16:21:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051455387-RemoveNearbyIndels 2022-02-07T16:24:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051456667-CompareDuplicatesSpark-BETA 2022-02-07T16:24:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051458715-MarkDuplicates-Picard 2022-02-07T16:21:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051460251-CreateSequenceDictionary-Picard 2022-02-07T16:24:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051461147-VcfToAdpc-Picard 2022-02-07T16:21:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051462299-GoodCigarReadFilter 2022-02-07T16:21:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051464219-PostprocessGermlineCNVCalls 2022-02-07T16:24:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051465499-NotSupplementaryAlignmentReadFilter 2022-02-07T16:21:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051467035-FilterAlignmentArtifacts-EXPERIMENTAL 2022-02-07T16:24:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051468315-PairedReadFilter 2022-02-07T16:21:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051471643-GetPileupSummaries 2022-10-12T07:08:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051473691-VariantFiltration 2022-02-07T16:24:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051474587-LikelihoodRankSumTest 2022-02-07T16:22:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051493787-MappingQualityZero 2022-02-07T16:22:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051495707-BamIndexStats-Picard 2022-02-07T16:24:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051496859-CollectArraysVariantCallingMetrics-Picard 2022-02-07T16:24:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051497883-VcfFormatConverter-Picard 2022-02-07T16:25:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051502107-ApplyBQSRSpark-BETA 2022-02-07T16:25:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051503899-CollectMultipleMetrics-Picard 2022-02-07T16:25:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051505051-ExtractSVEvidenceSpark-BETA 2022-02-07T16:25:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051505947-CollectAllelicCounts 2022-02-07T16:25:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051507099-MethylationTypeCaller-EXPERIMENTAL 2022-02-07T16:25:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051508251-PreprocessIntervals 2022-02-07T16:25:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051509403-CombineGenotypingArrayVcfs-Picard 2022-02-07T16:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051510683-FixMateInformation-Picard 2022-02-07T16:22:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051511835-PrintVariantsSpark 2022-02-07T16:25:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051513371-SamToFastq-Picard 2022-02-07T16:25:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051514907-CollectIlluminaBasecallingMetrics-Picard 2022-02-07T16:22:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051515931-FuncotatorDataSourceDownloader 2022-02-07T16:22:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051516955-CollectRnaSeqMetrics-Picard 2022-02-07T16:22:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051517979-GatherVcfsCloud-BETA 2022-02-07T16:22:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051520411-IntervalOverlapReadFilter 2022-02-07T16:22:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051521819-VariantRecalibrator 2022-02-07T16:25:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051523995-StructuralVariationDiscoveryPipelineSpark-BETA 2022-02-07T16:25:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051525147-EvaluateInfoFieldConcordance-BETA 2022-02-07T16:25:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051526171-SplitNCigarReads 2022-02-07T16:25:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051527579-PileupSpark-BETA 2022-02-07T16:25:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051530395-SplitVcfs-Picard 2022-02-07T16:25:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051532315-CNNVariantTrain-EXPERIMENTAL 2022-02-07T16:25:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051537563-AnalyzeSaturationMutagenesis-BETA 2022-02-07T16:25:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051538715-AS-QualByDepth 2022-02-07T16:25:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051539995-FragmentLengthReadFilter 2022-02-07T16:23:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051541019-CollectRrbsMetrics-Picard 2022-02-07T16:23:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051542299-NotSecondaryAlignmentReadFilter 2022-02-07T16:23:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051543451-ShiftFasta-BETA 2022-02-07T16:25:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051544475-MetricsReadFilter 2022-02-07T16:23:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051545883-AlleleFraction 2022-02-07T16:23:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051547291-OrientationBiasReadCounts 2022-02-07T16:23:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051548571-RenameSampleInVcf-Picard 2022-02-07T16:25:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051551643-CheckTerminatorBlock-Picard 2022-02-07T16:23:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4418051552667-ReadLengthReadFilter 2022-02-07T16:23:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054202139-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2022-02-07T16:23:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054204443-NonChimericOriginalAlignmentReadFilter 2022-02-07T16:20:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054206747-SampleReadFilter 2022-02-07T16:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054208155-Funcotator 2022-02-07T16:23:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054209435-CollectQualityYieldMetrics-Picard 2022-02-07T16:20:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054210971-CalcMetadataSpark-BETA 2022-02-07T16:23:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054214811-FilterVcf-Picard 2022-02-07T16:20:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054215835-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2022-02-07T16:23:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054217115-CountReads 2022-02-07T16:23:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054218779-EstimateLibraryComplexity-Picard 2022-02-07T16:20:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054221083-NotDuplicateReadFilter 2022-02-07T16:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054223003-VariantAnnotator 2022-02-07T16:23:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054229403-DetermineGermlineContigPloidy 2022-02-07T16:20:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054230939-MappingQuality 2022-02-07T16:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054232859-AS-RMSMappingQuality 2022-02-07T16:20:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054234267-CountVariantsSpark 2022-02-07T16:20:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054235419-IlluminaBasecallsToFastq-Picard 2022-02-07T16:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054237211-GeneExpressionEvaluation-BETA 2022-02-07T16:24:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054239131-CollectSamErrorMetrics-Picard 2022-02-07T16:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054240155-MarkDuplicatesSpark 2022-02-07T16:24:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054242715-DepthPerAlleleBySample 2022-02-07T16:20:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054244123-SetNmMdAndUqTags-Picard 2022-02-07T16:24:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054248091-CollectAlignmentSummaryMetrics-Picard 2022-02-07T16:20:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054249115-AnnotateVcfWithBamDepth 2022-02-07T16:24:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054250523-ExtractSequences-Picard 2022-02-07T16:24:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054251803-MarkDuplicatesWithMateCigar-Picard 2022-02-07T16:24:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054253211-CalculateContamination 2022-02-07T16:24:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054255003-MakeSitesOnlyVcf-Picard 2022-02-07T16:24:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054256411-LearnReadOrientationModel 2022-02-07T16:21:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054257691-CollectReadCounts 2022-02-07T16:24:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054263323-FilterIntervals 2022-02-07T16:21:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054264219-MappingQualityRankSumTest 2022-02-07T16:21:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054265499-CollectJumpingLibraryMetrics-Picard 2022-02-07T16:21:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054267035-ComposeSTRTableFile 2022-02-07T16:24:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054268699-FilterMutectCalls 2022-02-07T16:24:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054270107-SelectVariants 2022-02-07T16:24:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054271131-IlluminaBasecallsToSam-Picard 2022-02-07T16:21:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054272667-MappingQualityReadFilter 2022-02-07T16:24:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054274331-PlatformUnitReadFilter 2022-02-07T16:21:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054275355-CreateBafRegressMetricsFile-Picard 2022-02-07T16:21:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054279579-CreateHadoopBamSplittingIndex-BETA 2022-02-07T16:21:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054280731-MateDistantReadFilter 2022-02-07T16:24:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054282139-ValidAlignmentStartReadFilter 2022-02-07T16:24:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054284955-MarkIlluminaAdapters-Picard 2022-02-07T16:24:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054286107-SampleList 2022-02-07T16:21:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054288283-MatchingBasesAndQualsReadFilter 2022-02-07T16:21:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054290075-MeanQualityByCycleSpark-BETA 2022-02-07T16:24:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054291867-CollectBaseDistributionByCycle-Picard 2022-02-07T16:21:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054293275-MergeBamAlignment-Picard 2022-02-07T16:21:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054297627-FixMisencodedBaseQualityReads 2022-02-07T16:24:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054298907-ModelSegments 2022-02-07T16:24:38Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054300315-RevertSamSpark-BETA 2022-02-07T16:24:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054305819-BedToIntervalList-Picard 2022-02-07T16:24:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054307227-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2022-02-07T16:24:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054310555-AllelePseudoDepth 2022-02-07T16:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054311451-PositionBasedDownsampleSam-Picard 2022-02-07T16:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054312731-ReorderSam-Picard 2022-02-07T16:21:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054314395-GenotypeSummaries 2022-02-07T16:21:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054315547-FlagStatSpark 2022-02-07T16:24:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054316571-CollectWgsMetrics-Picard 2022-02-07T16:21:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054317723-AS-ReadPosRankSumTest 2022-02-07T16:21:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054320923-BaseRecalibrator 2022-02-07T16:24:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054322203-GatherTranches-BETA 2022-02-07T16:22:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054323739-DownsampleSam-Picard 2022-02-07T16:24:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054325659-ClippingRankSumTest 2022-02-07T16:22:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054327195-CompareSAMs-Picard 2022-02-07T16:24:50Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054328091-BQSRPipelineSpark-BETA 2022-02-07T16:24:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054329499-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2024-04-17T21:36:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054331675-BaseQualityRankSumTest 2022-02-07T16:22:10Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054332571-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2022-02-07T16:24:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054333595-IntervalListToBed-Picard 2022-02-07T16:22:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054336411-PrintSVEvidence-EXPERIMENTAL 2022-02-07T16:24:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054337819-GermlineCNVCaller 2022-02-07T16:22:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054338843-UpdateVcfSequenceDictionary-Picard 2022-02-07T16:22:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054339995-CallCopyRatioSegments 2022-02-07T16:22:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054340891-ScatterIntervalsByNs-Picard 2022-02-07T16:24:56Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054342427-PlatformReadFilter 2022-02-07T16:22:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054345115-CombineGVCFs 2022-02-07T16:25:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054346395-CollectGcBiasMetrics-Picard 2022-02-07T16:22:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054348187-AddOATag-Picard 2022-02-07T16:25:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054350107-Coverage 2022-02-07T16:22:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054351003-ReadStrandFilter 2022-02-07T16:22:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054352027-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2022-02-07T16:22:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054353307-MergeVcfs-Picard 2022-02-07T16:25:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054355227-CNNScoreVariants 2022-02-07T16:25:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054357787-QualityScoreDistribution-Picard 2022-02-07T16:22:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054360347-ValidateSamFile-Picard 2022-02-07T16:22:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054361243-BpmToNormalizationManifestCsv-Picard 2022-02-07T16:25:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054362779-ReadGroupBlackListReadFilter 2022-02-07T16:22:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054364571-ConvertHeaderlessHadoopBamShardToBam-BETA 2022-02-07T16:22:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054366363-AnnotateIntervals 2022-02-07T16:25:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054367643-SplitReads 2022-02-07T16:25:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054369691-BaseQuality 2022-02-07T16:22:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054370971-NonZeroReferenceLengthAlignmentReadFilter 2022-02-07T16:22:55Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054371867-CollectBaseDistributionByCycleSpark-BETA 2022-02-07T16:25:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054373019-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2022-02-07T16:25:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054374043-PlotDenoisedCopyRatios 2022-02-07T16:22:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054374939-SplitIntervals 2022-02-07T16:25:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054376475-NonZeroFragmentLengthReadFilter 2022-02-07T16:23:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054381979-ProperlyPairedReadFilter 2022-02-07T16:23:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054384027-GenotypeGVCFs 2022-02-07T16:25:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054385563-TandemRepeat 2022-02-07T16:23:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054386971-AddCommentsToBam-Picard 2022-02-07T16:25:33Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054392219-FindMendelianViolations-Picard 2022-02-07T16:25:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054394139-ReferenceBases 2022-02-07T16:23:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054396187-ConvertSequencingArtifactToOxoG-Picard 2022-02-07T16:23:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054397979-AssemblyComplexity 2022-02-07T16:23:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054399643-ReadAnonymizer-EXPERIMENTAL 2022-02-07T16:25:42Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054400795-MappingQualityAvailableReadFilter 2022-02-07T16:23:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054401691-CreateReadCountPanelOfNormals 2022-02-07T16:23:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054402843-CollectDuplicateMetrics-Picard 2022-02-07T16:23:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054405019-CalibrateDragstrModel 2022-02-07T16:25:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054406939-GtcToVcf-Picard 2022-02-07T16:23:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4418054408219-CleanSam-Picard 2022-02-07T16:23:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062650523-ChromosomeCounts 2022-02-07T16:20:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062651547-LibraryReadFilter 2022-02-07T16:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062653211-MeanQualityByCycle-Picard 2022-02-07T16:23:36Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062655259-OverclippedReadFilter 2022-02-07T16:20:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062657563-WellformedReadFilter 2022-02-07T16:23:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062659611-RMSMappingQuality 2022-02-07T16:20:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062660635-FirstOfPairReadFilter 2022-02-07T16:20:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062662555-SecondOfPairReadFilter 2022-02-07T16:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062665243-FixVcfHeader-Picard 2022-02-07T16:23:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062667035-LiftOverIntervalList-Picard 2022-02-07T16:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062670875-MergePedIntoVcf-Picard 2022-02-07T16:20:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062672027-CollectMultipleMetricsSpark-BETA 2022-02-07T16:23:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062673691-CountBases 2022-02-07T16:23:53Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062674971-StrandOddsRatio 2022-02-07T16:20:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062676123-HasReadGroupReadFilter 2022-02-07T16:20:37Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062678811-UniqueAltReadCount 2022-02-07T16:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062679835-QualByDepth 2022-02-07T16:20:40Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062680731-VariantsToTable 2022-02-07T16:23:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062682011-NormalizeFasta-Picard 2022-02-07T16:23:57Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062683803-CNNVariantWriteTensors-EXPERIMENTAL 2022-02-07T16:23:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062684827-UpdateVCFSequenceDictionary 2022-02-07T16:23:59Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062685979-SamFormatConverter-Picard 2022-02-07T16:20:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062687003-FisherStrand 2022-02-07T16:20:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062688027-ClipReads 2022-02-07T16:24:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062689051-SoftClippedReadFilter 2022-02-07T16:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062690075-GetSampleName 2022-02-07T16:24:02Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062691483-CalculateReadGroupChecksum-Picard 2022-02-07T16:24:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062692379-CompareMetrics-Picard 2022-02-07T16:24:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062693915-FuncotateSegments-BETA 2022-02-07T16:24:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062695195-PathSeqBuildReferenceTaxonomy 2022-02-07T16:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062696731-BwaSpark-BETA 2022-02-07T16:24:07Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062697883-CollectSequencingArtifactMetrics-Picard 2022-02-07T16:20:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062699419-GatherBQSRReports 2022-02-07T16:21:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062700443-ApplyBQSR 2022-02-07T16:24:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062701339-CpxVariantReInterpreterSpark-BETA 2022-02-07T16:24:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062703131-CollectInsertSizeMetrics-Picard 2022-02-07T16:21:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062704027-StrandBiasBySample 2022-02-07T16:21:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062705051-FragmentDepthPerAlleleBySample 2022-02-07T16:21:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062706459-SortSamSpark-BETA 2022-02-07T16:24:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062707867-LeftAlignIndels 2022-02-07T16:24:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062709019-MappingQualityNotZeroReadFilter 2022-02-07T16:21:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062709915-HaplotypeCallerSpark-BETA 2022-02-07T16:24:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062710939-SplitSamByNumberOfReads-Picard 2022-02-07T16:24:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062712731-NonNFastaSize-Picard 2022-02-07T16:24:19Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062713883-CalculateMixingFractions 2022-02-07T16:24:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062715163-AccumulateVariantCallingMetrics-Picard 2022-02-07T16:21:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062717083-ReadGroupReadFilter 2022-02-07T16:21:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062718107-CollectQualityYieldMetricsSpark-BETA 2022-02-07T16:24:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062719899-HaplotypeCaller 2022-02-07T16:24:28Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062721051-ReplaceSamHeader-Picard 2022-02-07T16:24:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062722075-CountFalsePositives-BETA 2022-02-07T16:24:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062723099-MateUnmappedAndUnmappedReadFilter 2022-02-07T16:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062727707-VcfToIntervalList-Picard 2022-02-07T16:24:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062729371-SetNmAndUqTags-Picard 2022-02-07T16:24:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062730267-PathSeqBwaSpark 2024-03-19T07:57:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062732827-CollectTargetedPcrMetrics-Picard 2022-02-07T16:24:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062738331-ExtractIlluminaBarcodes-Picard 2022-02-07T16:21:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062739611-AmbiguousBaseReadFilter 2022-02-07T16:21:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062740635-CollectRawWgsMetrics-Picard 2022-02-07T16:24:41Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062741787-OriginalAlignment 2022-02-07T16:21:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062744219-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-02-07T16:21:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062750235-FifoBuffer-Picard 2022-02-07T16:22:00Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062751131-ExcessHet 2022-02-07T16:22:01Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062753435-RevertBaseQualityScores 2022-02-07T16:24:49Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062758427-PossibleDeNovo 2022-02-07T16:22:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062759707-CollectInsertSizeMetricsSpark-BETA 2022-02-07T16:24:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062760859-DenoiseReadCounts 2022-02-07T16:22:09Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062763803-ApplyVQSR 2022-02-07T16:24:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062765083-ReadNameReadFilter 2022-02-07T16:22:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062769947-AS-InbreedingCoeff 2022-02-07T16:22:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062771227-Mutect2 2022-02-07T16:24:58Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062772891-AddOrReplaceReadGroups-Picard 2022-02-07T16:22:21Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062773915-PlotModeledSegments 2022-02-07T16:22:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062775963-CollectVariantCallingMetrics-Picard 2022-02-07T16:22:22Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062778011-LocalAssembler-BETA 2022-02-07T16:25:03Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062779035-LiftoverVcf-Picard 2022-02-07T16:25:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062781339-ReadPosition 2022-02-07T16:22:25Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062783259-MateOnSameContigOrNoMappedMateReadFilter 2022-02-07T16:25:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062784795-CalculateGenotypePosteriors 2022-02-07T16:25:06Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062785947-ValidateVariants 2022-02-07T16:25:08Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062788379-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2022-02-07T16:22:34Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062790171-PrintDistantMates 2022-02-07T16:25:11Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062791195-FlagStat 2022-02-07T16:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062792475-BaitDesigner-Picard 2022-02-07T16:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062793499-InbreedingCoeff 2022-02-07T16:22:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062794651-ReadLengthEqualsCigarLengthReadFilter 2022-02-07T16:25:13Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062795547-SortVcf-Picard 2022-02-07T16:25:14Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062797211-FastqToSam-Picard 2022-02-07T16:25:15Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062801691-SortSam-Picard 2022-02-07T16:25:16Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062802971-MergeSamFiles-Picard 2022-02-07T16:25:18Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062804379-PathSeqScoreSpark 2022-02-07T16:25:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062805403-RevertSam-Picard 2022-02-07T16:25:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062806299-PassesVendorQualityCheckReadFilter 2022-02-07T16:22:51Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062807323-AS-MappingQualityRankSumTest 2022-02-07T16:22:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062808475-ReadPosRankSumTest 2022-02-07T16:22:52Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062809627-SeqIsStoredReadFilter 2022-02-07T16:22:54Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062811163-PathSeqFilterSpark 2022-02-07T16:25:24Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062812315-FastaAlternateReferenceMaker 2022-02-07T16:25:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062813211-UnmarkDuplicates 2022-02-07T16:25:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062816667-DepthOfCoverage-BETA 2025-03-06T08:26:27Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062818203-CigarContainsNoNOperator 2022-02-07T16:23:05Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062819227-FilterFuncotations-EXPERIMENTAL 2022-02-07T16:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062820379-SplitSamByLibrary-Picard 2022-02-07T16:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062821531-CrosscheckFingerprints-Picard 2022-02-07T16:25:31Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062822939-FindBadGenomicKmersSpark-BETA 2022-02-07T16:25:32Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062824603-AS-BaseQualityRankSumTest 2022-02-07T16:23:12Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062825499-Concordance 2022-02-07T16:25:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062827291-BuildBamIndex-Picard 2022-02-07T16:25:35Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062828955-IndexFeatureFile 2022-02-07T16:23:17Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062829851-ValidAlignmentEndReadFilter 2022-02-07T16:25:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062830875-FastaReferenceMaker 2022-02-07T16:25:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062831771-QualityScoreDistributionSpark-BETA 2022-02-07T16:25:39Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062833051-DepthPerSampleHC 2022-02-07T16:23:20Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062834843-CountNs 2022-02-07T16:23:23Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062837147-CollectOxoGMetrics-Picard 2022-02-07T16:23:26Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062838427-CountReadsSpark 2022-02-07T16:25:43Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062839579-CountBasesSpark 2022-02-07T16:25:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062840603-PrintReadsSpark 2022-02-07T16:25:44Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062841499-ASEReadCounter 2022-02-07T16:25:45Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062842779-FilterVariantTranches 2022-02-07T16:25:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062843675-CreateSomaticPanelOfNormals-BETA 2022-02-07T16:25:46Z https://gatk.broadinstitute.org/hc/en-us/articles/4418062844699-CheckPileup 2022-02-07T16:25:47Z https://gatk.broadinstitute.org/hc/en-us/articles/4524513257499-GATK-on-the-cloud-with-Terra 2024-07-01T17:07:04Z https://gatk.broadinstitute.org/hc/en-us/articles/4636646119579-Please-update-your-GATK-Important-information-about-GATK-4-2-6-1 2024-07-01T17:07:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257792401179-VerifyIDIntensityContaminationMetrics 2022-04-08T20:52:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5257792668827-SecondOfPairReadFilter 2022-04-08T20:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5257792781083-RnaSeqMetrics 2022-04-08T20:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257793107995-NotDuplicateReadFilter 2022-04-08T20:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257793287579-PrimaryLineReadFilter 2022-04-08T20:53:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257793804443-GeneExpressionEvaluation-BETA 2022-04-08T20:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5257793899931-GetSampleName 2022-04-08T20:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794151451-CompareBaseQualities 2022-04-08T20:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794165787-BwaSpark-BETA 2022-04-08T20:57:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794200091-SamComparisonMetric 2022-04-08T20:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794337435-CalculateContamination 2022-04-08T20:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794477083-IntervalListTools-Picard 2022-04-08T20:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794517915-FragmentDepthPerAlleleBySample 2022-04-08T20:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794816539-NonNFastaSize-Picard 2022-04-08T20:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5257794851739-FingerprintMetrics 2022-04-08T20:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826157339-SampleReadFilter 2022-04-08T20:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826440475-GcBiasSummaryMetrics 2022-04-08T20:52:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826521499-FixVcfHeader-Picard 2022-04-08T20:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826540187-CollectHsMetrics-Picard 2022-04-08T20:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826618267-GnarlyGenotyper-BETA 2022-04-08T20:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826671387-EstimateLibraryComplexity-Picard 2022-04-08T20:52:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826692251-PrintReadsHeader 2022-04-08T20:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5257826784411-AllowAllReadsReadFilter 2022-04-08T20:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257827311003-MappingQuality 2022-04-08T20:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257827326747-QualByDepth 2022-04-08T20:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257827427995-PFFailSummaryMetric 2022-04-08T20:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5257827454491-CNNVariantWriteTensors-EXPERIMENTAL 2022-04-08T20:57:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257827707291-ClipReads 2022-04-08T20:57:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5257827805211-MarkDuplicatesSpark 2022-04-08T20:57:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257827921691-CompareMetrics-Picard 2022-04-08T20:57:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5257828008731-BaitBiasSummaryMetrics 2022-04-08T20:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5257828242971-GenotypeConcordanceContingencyMetrics 2022-04-08T20:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257828278427-GatherVcfs-Picard 2022-04-08T20:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257842769307-GenotypeConcordance-Picard 2022-04-08T20:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257842792859-Pileup 2022-04-08T20:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5257842898331-NotProperlyPairedReadFilter 2022-04-08T20:52:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5257842950299-BarcodeMetric 2022-04-08T20:52:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257843168027-PathSeqPipelineSpark 2022-04-08T20:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257843295899-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2022-04-08T20:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257843464603-AccumulateQualityYieldMetrics-Picard 2022-04-08T20:52:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5257843670811-CountVariants 2022-04-08T20:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5257844029595-MergePedIntoVcf-Picard 2022-04-08T20:53:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5257844136475-CollectMultipleMetricsSpark-BETA 2022-04-08T20:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257844179611-CountBases 2022-04-08T20:57:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5257844413723-FindBreakpointEvidenceSpark-BETA 2022-04-08T20:57:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5257845017883-ClusterCrosscheckMetrics-Picard 2022-04-08T20:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5257845053211-CollectSamErrorMetrics-Picard 2022-04-08T20:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257845147931-DepthPerAlleleBySample 2022-04-08T20:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5257845198619-GcBiasMetrics 2022-04-08T20:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257848396315-LibraryReadFilter 2022-04-08T20:52:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5257848448411-NonChimericOriginalAlignmentReadFilter 2022-04-08T20:52:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849208091-VariantEval-BETA 2022-04-08T20:52:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849382811-JumpingLibraryMetrics 2022-04-08T20:52:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849503259-ViewSam-Picard 2022-04-08T20:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849646491-LiftOverIntervalList-Picard 2022-04-08T20:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849680923-OverlappingErrorMetric 2022-04-08T20:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849737499-VariantCallingSummaryMetrics 2022-04-08T20:53:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849757595-PreAdapterSummaryMetrics 2022-04-08T20:53:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849789339-ArraysControlCodesSummaryMetrics 2022-04-08T20:53:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257849847195-VariantAnnotator 2022-04-08T20:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5257850198043-HasReadGroupReadFilter 2022-04-08T20:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5257850368539-VariantsToTable 2022-04-08T20:57:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257850419227-NormalizeFasta-Picard 2022-04-08T20:57:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257850915739-SoftClippedReadFilter 2022-04-08T20:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257851036059-CalculateReadGroupChecksum-Picard 2022-04-08T20:57:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257851180827-FuncotateSegments-BETA 2022-04-08T20:57:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257851531291-CollectAlignmentSummaryMetrics-Picard 2022-04-08T20:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257851563419-AnnotateVcfWithBamDepth 2022-04-08T20:57:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5257851829787-PathSeqBuildKmers 2022-04-08T20:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257852051227-InsertSizeMetrics 2022-04-08T20:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257852072219-SortSamSpark-BETA 2022-04-08T20:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5257852412827-HsMetrics 2022-04-08T20:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257852441883-ComposeSTRTableFile 2022-04-08T20:57:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5257852670107-SelectVariants 2022-04-08T20:57:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257852705819-AccumulateVariantCallingMetrics-Picard 2022-04-08T20:54:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5257852989467-PrintReads 2022-04-08T20:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5257853025563-BwaAndMarkDuplicatesPipelineSpark-BETA 2022-04-08T20:57:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5257853376027-CollectIlluminaLaneMetrics-Picard 2022-04-08T20:54:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5257853396507-CountBasesInReference 2022-04-08T20:57:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856379035-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2022-04-08T20:52:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856434843-CollectHiSeqXPfFailMetrics-Picard 2022-04-08T20:52:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856577179-BwaMemIndexImageCreator 2022-04-08T20:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856789787-AnalyzeCovariates 2022-04-08T20:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856846363-FirstOfPairReadFilter 2022-04-08T20:52:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856885659-CollectQualityYieldMetrics-Picard 2022-04-08T20:52:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856916635-CalcMetadataSpark-BETA 2022-04-08T20:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856971163-AS-StrandOddsRatio 2022-04-08T20:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257856993435-FilterVcf-Picard 2022-04-08T20:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257857182491-IlluminaBasecallingMetrics 2022-04-08T20:52:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257857510811-BamToBfq-Picard 2022-04-08T20:53:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5257857696795-BafRegressMetrics 2022-04-08T20:53:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257857769883-StrandOddsRatio 2022-04-08T20:53:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257857860123-MendelianViolationMetrics 2022-04-08T20:53:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5257857881371-CheckFingerprint-Picard 2022-04-08T20:53:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5257857942171-DetermineGermlineContigPloidy 2022-04-08T20:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5257858262299-CountVariantsSpark 2022-04-08T20:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5257858295963-UpdateVCFSequenceDictionary 2022-04-08T20:57:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257858383899-PostProcessReadsForRSEM-BETA 2022-04-08T20:57:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5257858793371-GatherBamFiles-Picard 2022-04-08T20:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5257858907163-PathSeqBuildReferenceTaxonomy 2022-04-08T20:53:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5257858948507-AS-FisherStrand 2022-04-08T20:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5257859174171-MappedReadFilter 2022-04-08T20:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5257859230491-MarkDuplicatesWithMateCigar-Picard 2022-04-08T20:57:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5257859270811-GatherBQSRReports 2022-04-08T20:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257859334043-ApplyBQSR 2022-04-08T20:57:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257859378715-CpxVariantReInterpreterSpark-BETA 2022-04-08T20:57:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257859775131-GetNormalArtifactData 2022-04-08T20:57:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5257859825691-CollectJumpingLibraryMetrics-Picard 2022-04-08T20:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5257860190619-SVCluster-BETA 2022-04-08T20:57:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5257860212379-ReadGroupReadFilter 2022-04-08T20:54:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257860255003-MappingQualityReadFilter 2022-04-08T20:57:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5257860298395-GenomicsDBImport 2022-04-08T20:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257860353435-PlatformUnitReadFilter 2022-04-08T20:54:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257860991643-VcfToIntervalList-Picard 2022-04-08T20:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257861482651-FixMisencodedBaseQualityReads 2022-04-08T20:57:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257861552539-FeaturizedReadSets 2022-04-08T20:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257861627547-RevertSamSpark-BETA 2022-04-08T20:57:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5257861662107-ExtractIlluminaBarcodes-Picard 2022-04-08T20:54:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5257861799579-RemoveNearbyIndels 2022-04-08T20:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862083611-IlluminaBasecallsToSam-Picard 2022-04-08T20:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862298651-CreateHadoopBamSplittingIndex-BETA 2022-04-08T20:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862368795-MateDistantReadFilter 2022-04-08T20:57:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862382875-HaplotypeCaller 2022-04-08T20:57:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862419099-ValidAlignmentStartReadFilter 2022-04-08T20:57:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862466075-ReplaceSamHeader-Picard 2022-04-08T20:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862566811-ClusteredCrosscheckMetric 2022-04-08T20:54:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862603931-SetNmAndUqTags-Picard 2022-04-08T20:57:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862649243-MarkIlluminaAdapters-Picard 2022-04-08T20:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862720795-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2022-04-08T20:57:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257862811547-CollectBaseDistributionByCycle-Picard 2022-04-08T20:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5257863305499-NotSupplementaryAlignmentReadFilter 2022-04-08T20:54:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5257863504923-VariantFiltration 2022-04-08T20:58:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5257863684123-BQSRPipelineSpark-BETA 2022-04-08T20:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257863787547-PossibleDeNovo 2022-04-08T20:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864010907-MappingQualityZero 2022-04-08T20:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864237467-VcfFormatConverter-Picard 2022-04-08T20:58:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864317467-CollectVariantCallingMetrics-Picard 2022-04-08T20:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864350875-CombineGVCFs 2022-04-08T20:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864435995-AddOATag-Picard 2022-04-08T20:58:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864518811-TargetedPcrMetrics 2022-04-08T20:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864581787-CalculateGenotypePosteriors 2022-04-08T20:58:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5257864682267-ExtractSVEvidenceSpark-BETA 2022-04-08T20:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865117083-IndependentReplicateMetric 2022-04-08T20:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865147675-ReadGroupBlackListReadFilter 2022-04-08T20:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865382043-PathSeqScoreSpark 2022-04-08T20:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865399451-RevertSam-Picard 2022-04-08T20:58:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865411099-PassesVendorQualityCheckReadFilter 2022-04-08T20:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865725467-SplitNCigarReads 2022-04-08T20:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865797531-BaseErrorMetric 2022-04-08T20:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865813275-CigarContainsNoNOperator 2022-04-08T20:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865879707-FilterFuncotations-EXPERIMENTAL 2022-04-08T20:59:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257865942427-CNNVariantTrain-EXPERIMENTAL 2022-04-08T20:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866217243-FragmentLengthReadFilter 2022-04-08T20:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866293019-FindMendelianViolations-Picard 2022-04-08T20:59:08Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866321563-WgsMetricsWithNonZeroCoverage 2022-04-08T20:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866499483-OrientationBiasReadCounts 2022-04-08T20:56:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866519963-AssemblyComplexity 2022-04-08T20:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866637339-CreateReadCountPanelOfNormals 2022-04-08T20:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866708123-CountBasesSpark 2022-04-08T20:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866801051-CreateSomaticPanelOfNormals-BETA 2022-04-08T20:59:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5257866860955-CheckTerminatorBlock-Picard 2022-04-08T20:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5257871491483-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2022-04-08T20:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5257871526939-ChromosomeCounts 2022-04-08T20:52:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5257871647259-MeanQualityByCycle-Picard 2022-04-08T20:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5257871746971-OverclippedReadFilter 2022-04-08T20:52:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257871843739-ExcessiveEndClippedReadFilter 2022-04-08T20:52:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257871888795-WellformedReadFilter 2022-04-08T20:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257871982747-RMSMappingQuality 2022-04-08T20:52:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5257872040731-Funcotator 2022-04-08T20:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257872251803-AlignmentAgreesWithHeaderReadFilter 2022-04-08T20:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5257872511771-CountReads 2022-04-08T20:56:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257872783899-AnnotateVcfWithExpectedAlleleFraction 2022-04-08T20:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257872822939-ErrorMetric 2022-04-08T20:52:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5257873079963-FilterSamReads-Picard 2022-04-08T20:56:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257873285659--Tool-Documentation-Index 2022-04-08T20:57:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5257873499547-UniqueAltReadCount 2022-04-08T20:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257873649179-AS-RMSMappingQuality 2022-04-08T20:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257873790363-IlluminaBasecallsToFastq-Picard 2022-04-08T20:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257873821083-SamFormatConverter-Picard 2022-04-08T20:53:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5257873894939-FisherStrand 2022-04-08T20:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5257874207131-SetNmMdAndUqTags-Picard 2022-04-08T20:57:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257874793627-ExtractSequences-Picard 2022-04-08T20:57:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5257875070619-MakeSitesOnlyVcf-Picard 2022-04-08T20:57:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5257875204891-LearnReadOrientationModel 2022-04-08T20:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257875400091-FilterIntervals 2022-04-08T20:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257875563035-HaplotypeCallerSpark-BETA 2022-04-08T20:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5257875815707-BaseRecalibratorSpark-BETA 2022-04-08T20:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5257876412059-AlignmentSummaryMetrics 2022-04-08T20:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5257876637723-CountFalsePositives-BETA 2022-04-08T20:57:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257876662939-MateUnmappedAndUnmappedReadFilter 2022-04-08T20:54:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257876986523-MeanQualityByCycleSpark-BETA 2022-04-08T20:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877037979-CheckIlluminaDirectory-Picard 2022-04-08T20:57:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877325339-LeftAlignAndTrimVariants 2022-04-08T20:57:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877524763-AmbiguousBaseReadFilter 2022-04-08T20:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877703451-OriginalAlignment 2022-04-08T20:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877746203-MarkDuplicates-Picard 2022-04-08T20:54:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877867803-AllelePseudoDepth 2022-04-08T20:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877935771-PreAdapterDetailMetrics 2022-04-08T20:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257877949083-ReorderSam-Picard 2022-04-08T20:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257878057755-BaseDistributionByCycleMetrics 2022-04-08T20:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257878094747-FlagStatSpark 2022-04-08T20:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257878563995-CompareSAMs-Picard 2022-04-08T20:58:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257879060251-CollectReadCounts 2022-04-08T20:57:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257879162779-LeftAlignIndels 2022-04-08T20:57:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5257879222299-MappingQualityRankSumTest 2022-04-08T20:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257879342875-SplitSamByNumberOfReads-Picard 2022-04-08T20:57:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5257879538715-CalculateMixingFractions 2022-04-08T20:57:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5257879820827-CreateBafRegressMetricsFile-Picard 2022-04-08T20:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257880337051-PathSeqBwaSpark 2022-04-08T20:57:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5257880489371-FragmentLength 2022-04-08T20:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5257880580379-RrbsSummaryMetrics 2022-04-08T20:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257880608539-ReblockGVCF 2022-04-08T20:57:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5257880651931-MergeBamAlignment-Picard 2022-04-08T20:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257880714139-ModelSegments 2022-04-08T20:57:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5257881423387-CollectWgsMetrics-Picard 2022-04-08T20:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257881456539-UmiMetrics 2022-04-08T20:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257881496475-PairedReadFilter 2022-04-08T20:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5257881589275-FifoBuffer-Picard 2022-04-08T20:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5257881614491-ExcessHet 2022-04-08T20:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5257881715611-RevertBaseQualityScores 2022-04-08T20:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882005275-CollectInsertSizeMetricsSpark-BETA 2022-04-08T20:58:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882025883-DenoiseReadCounts 2022-04-08T20:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882033563-BaseQualityRankSumTest 2022-04-08T20:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882061083-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2022-04-08T20:58:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882071323-IntervalListToBed-Picard 2022-04-08T20:55:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882158235-PrintSVEvidence-EXPERIMENTAL 2022-04-08T20:58:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882195483-GermlineCNVCaller 2022-04-08T20:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882312859-CallCopyRatioSegments 2022-04-08T20:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882372635-QualityYieldMetrics 2022-04-08T20:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882584475-AddOrReplaceReadGroups-Picard 2022-04-08T20:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882756763-CollectGcBiasMetrics-Picard 2022-04-08T20:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882823579-ArraysVariantCallingSummaryMetrics 2022-04-08T20:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5257882998811-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2022-04-08T20:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5257883249691-CpcgMetrics 2022-04-08T20:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257883376539-CombineGenotypingArrayVcfs-Picard 2022-04-08T20:58:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5257883451547-InbreedingCoeff 2022-04-08T20:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5257883521563-SortVcf-Picard 2022-04-08T20:58:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257883563419-PrintVariantsSpark 2022-04-08T20:58:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257883608091-BpmToNormalizationManifestCsv-Picard 2022-04-08T20:58:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5257884155803-BaseQuality 2022-04-08T20:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257884165275-SeqIsStoredReadFilter 2022-04-08T20:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257884176411-IntervalOverlapReadFilter 2022-04-08T20:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257884511771-ProperlyPairedReadFilter 2022-04-08T20:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885107739-NotSecondaryAlignmentReadFilter 2022-04-08T20:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885179035-ShiftFasta-BETA 2022-04-08T20:59:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885231899-MetricsReadFilter 2022-04-08T20:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885274267-FastaReferenceMaker 2022-04-08T20:59:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885334811-AlleleFraction 2022-04-08T20:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885626907-ASEReadCounter 2022-07-08T21:03:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885670427-CalibrateDragstrModel 2022-04-08T20:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885705115-FilterVariantTranches 2022-04-08T20:59:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885802523-GtcToVcf-Picard 2022-04-08T20:56:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257885885339-CleanSam-Picard 2022-04-08T20:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257887276315-CalculateFingerprintMetrics-Picard 2022-04-08T20:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5257887478811-CollectSequencingArtifactMetrics-Picard 2022-04-08T20:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5257887867803-CollectInsertSizeMetrics-Picard 2022-04-08T20:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257887887259-StrandBiasBySample 2022-04-08T20:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257888253979-MappingQualityNotZeroReadFilter 2022-04-08T20:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5257888539931-MateDifferentStrandReadFilter 2022-04-08T20:57:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5257888603803-FilterMutectCalls 2022-04-08T20:57:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257888704155-BaitBiasDetailMetrics 2022-04-08T20:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257889004955-CollectQualityYieldMetricsSpark-BETA 2022-04-08T20:57:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257889151643-GenotypeConcordanceSummaryMetrics 2022-04-08T20:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257889332379-ReadsPipelineSpark-BETA 2022-04-08T20:57:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257889762587-SampleList 2022-04-08T20:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257889785371-MatchingBasesAndQualsReadFilter 2022-04-08T20:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257889949851-CollectTargetedPcrMetrics-Picard 2022-04-08T20:57:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5257890251547-PFFailDetailedMetric 2022-04-08T20:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5257890288795-BedToIntervalList-Picard 2022-04-08T20:57:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5257890363419-CollectRawWgsMetrics-Picard 2022-04-08T20:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257890472219-GoodCigarReadFilter 2022-04-08T20:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257890925467-GetPileupSummaries 2022-04-08T20:58:08Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891036955-LikelihoodRankSumTest 2022-04-08T20:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891054235-BaseRecalibrator 2022-04-08T20:58:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891113755-DownsampleSam-Picard 2022-04-08T20:58:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891174043-VariantCallingDetailMetrics 2022-04-08T20:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891291419-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-04-08T20:58:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891339035-TransferReadTags-EXPERIMENTAL 2022-04-08T20:58:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891734427-IlluminaLaneMetrics 2022-04-08T20:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891830171-CollectArraysVariantCallingMetrics-Picard 2022-04-08T20:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891839899-TargetMetrics 2022-04-08T20:55:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891901467-PlotModeledSegments 2022-04-08T20:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257891996187-LocalAssembler-BETA 2022-04-08T20:58:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257892139675-MateOnSameContigOrNoMappedMateReadFilter 2022-04-08T20:58:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5257892250011-ApplyBQSRSpark-BETA 2022-04-08T20:58:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5257892468123-ValidateVariants 2022-04-08T20:58:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257892554651-CNNScoreVariants 2022-04-08T20:58:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257892728731-PreprocessIntervals 2022-04-08T20:58:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5257892801819-BaitDesigner-Picard 2022-04-08T20:58:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5257892878619-FixMateInformation-Picard 2022-04-08T20:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5257893227163-CollectRnaSeqMetrics-Picard 2022-04-08T20:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257893248411-GatherVcfsCloud-BETA 2022-04-08T20:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257893583259-VariantRecalibrator 2022-04-08T20:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257893671195-PlotDenoisedCopyRatios 2022-04-08T20:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5257893718683-FastaAlternateReferenceMaker 2022-04-08T20:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5257893743387-UnmarkDuplicates 2022-04-08T20:58:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5257894485659-BuildBamIndex-Picard 2022-04-08T20:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257894517019-CollectRrbsMetrics-Picard 2022-04-08T20:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257894696859-IndexFeatureFile 2022-04-08T20:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257894832283-DepthPerSampleHC 2022-04-08T20:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5257895072539-MappingQualityAvailableReadFilter 2022-04-08T20:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5257895097627-CollectOxoGMetrics-Picard 2022-04-08T20:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5257895258139-PrintReadsSpark 2022-04-08T20:59:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257895777691-RrbsCpgDetailMetrics 2022-04-08T20:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257895943835-DuplicationMetrics 2022-04-08T20:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5257896191131-CompareDuplicatesSpark-BETA 2022-04-08T20:57:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257896241819-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2022-04-08T20:57:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257896318235-CreateSequenceDictionary-Picard 2022-04-08T20:58:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5257896330907-VcfToAdpc-Picard 2022-04-08T20:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257896520219-PostprocessGermlineCNVCalls 2022-04-08T20:58:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5257896560667-GenotypeSummaries 2022-04-08T20:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257896925723-GatherTranches-BETA 2022-04-08T20:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5257897096091-ArraysVariantCallingDetailMetrics 2022-04-08T20:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5257897474715-ErrorSummaryMetrics 2022-04-08T20:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257897530267-ScatterIntervalsByNs-Picard 2022-04-08T20:58:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5257897545115-AS-InbreedingCoeff 2022-04-08T20:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257897695387-Mutect2 2022-04-08T20:58:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257898237467-Coverage 2022-04-08T20:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5257898786587-PrintDistantMates 2022-04-08T20:58:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257898905883-IlluminaPhasingMetrics 2022-04-08T20:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5257898935835-ReadLengthEqualsCigarLengthReadFilter 2022-04-08T20:58:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899243803-SamToFastq-Picard 2022-04-08T20:58:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899291163-GcBiasDetailMetrics 2022-04-08T20:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899318811-CollectIlluminaBasecallingMetrics-Picard 2022-04-08T20:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899336731-FuncotatorDataSourceDownloader 2022-04-08T20:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899526811-SplitReads 2022-04-08T20:58:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899806875-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2022-04-08T20:58:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899878427-SplitIntervals 2022-04-08T20:58:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5257899991195-EvaluateInfoFieldConcordance-BETA 2022-04-08T20:58:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5257900485659-GenotypeGVCFs 2022-04-08T20:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5257900638491-FindBadGenomicKmersSpark-BETA 2022-04-08T20:59:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5257900736027-AnalyzeSaturationMutagenesis-BETA 2022-04-08T20:59:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257900764187-AS-QualByDepth 2022-04-08T20:59:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257901143451-IndelErrorMetric 2022-04-08T20:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5257901470363-CountNs 2022-04-08T20:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5257901676187-CountReadsSpark 2022-04-08T20:59:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5257901899163-CheckPileup 2022-04-08T20:59:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5257904044315-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-04-08T20:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5257904097179-PositionBasedDownsampleSam-Picard 2022-04-08T20:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5257904175131-RawWgsMetrics 2022-04-08T20:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5257904375707-FilterAlignmentArtifacts-EXPERIMENTAL 2022-04-08T20:58:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5257904474523-AS-ReadPosRankSumTest 2022-04-08T20:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5257904697115-GenotypeConcordanceDetailMetrics 2022-04-08T20:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5257904766363-ClippingRankSumTest 2022-04-08T20:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257905116571-ApplyVQSR 2022-04-08T20:58:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257905240731-UpdateVcfSequenceDictionary-Picard 2022-04-08T20:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5257905442459-PlatformReadFilter 2022-04-08T20:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257905531163-BamIndexStats-Picard 2022-04-08T20:58:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257905753627-TheoreticalSensitivityMetrics 2022-04-08T20:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5257905891227-LiftoverVcf-Picard 2022-04-08T20:58:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5257905982491-ReadPosition 2022-04-08T20:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257906054299-ReadStrandFilter 2022-04-08T20:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5257906204315-MergeVcfs-Picard 2022-04-08T20:58:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5257906395291-FingerprintingSummaryMetrics 2022-04-08T20:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5257906527131-FlagStat 2022-04-08T20:58:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257906722843-ValidateSamFile-Picard 2022-04-08T20:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5257906838811-FastqToSam-Picard 2022-04-08T20:58:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5257906962459-SortSam-Picard 2022-04-08T20:58:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907091227-MergeSamFiles-Picard 2022-04-08T20:58:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907317403-AS-MappingQualityRankSumTest 2022-04-08T20:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907355291-ReadPosRankSumTest 2022-04-08T20:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907480603-PathSeqFilterSpark 2022-04-08T20:58:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907625627-StructuralVariationDiscoveryPipelineSpark-BETA 2022-04-08T20:58:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907709211-DepthOfCoverage-BETA 2022-04-08T20:58:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907925403-SplitSamByLibrary-Picard 2022-04-08T20:59:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5257907948699-CrosscheckFingerprints-Picard 2022-04-08T20:59:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5257908020763-TandemRepeat 2022-04-08T20:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257908101403-AddCommentsToBam-Picard 2022-04-08T20:59:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5257908210715-AS-BaseQualityRankSumTest 2022-04-08T20:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257908243739-Concordance 2022-04-08T20:59:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5257908702491-FingerprintingDetailMetrics 2022-04-08T20:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5257908944411-RenameSampleInVcf-Picard 2022-04-08T20:59:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5257908984347-ReadAnonymizer-EXPERIMENTAL 2022-04-08T20:59:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5257909104411-CollectDuplicateMetrics-Picard 2022-04-08T20:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5257912633243-ReadNameReadFilter 2022-04-08T20:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5257913472283-CollectMultipleMetrics-Picard 2022-04-08T20:58:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5257913554331-CollectAllelicCounts 2022-04-08T20:58:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5257913637787-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2022-04-08T20:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5257913677211-MethylationTypeCaller-EXPERIMENTAL 2022-04-08T20:58:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5257913762331-QualityScoreDistribution-Picard 2022-04-08T20:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5257914107291-WgsMetrics 2022-04-08T20:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5257914251291-ConvertHeaderlessHadoopBamShardToBam-BETA 2022-04-08T20:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5257914351131-AnnotateIntervals 2022-04-08T20:58:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5257914681627-NonZeroReferenceLengthAlignmentReadFilter 2022-04-08T20:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5257914697755-CollectBaseDistributionByCycleSpark-BETA 2022-04-08T20:58:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5257915038875-NonZeroFragmentLengthReadFilter 2022-04-08T20:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5257915084955-PileupSpark-BETA 2022-04-08T20:59:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5257915159195-SplitVcfs-Picard 2022-04-08T20:59:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5257915975835-ReferenceBases 2022-04-08T20:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5257916048795-ValidAlignmentEndReadFilter 2022-04-08T20:59:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5257916115611-QualityScoreDistributionSpark-BETA 2022-04-08T20:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5257916186011-ConvertSequencingArtifactToOxoG-Picard 2022-04-08T20:56:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5257916708251-ReadLengthReadFilter 2022-04-08T20:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5334566940699-Troubleshooting-GATK-SV 2024-07-08T19:36:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5334587352219-How-to-interpret-SV-VCFs 2024-07-08T19:36:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5358808667419-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2022-04-13T20:17:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358808928923-MeanQualityByCycle-Picard 2022-04-13T20:17:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5358808976795-CollectHiSeqXPfFailMetrics-Picard 2022-04-13T20:13:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5358809216411-ExcessiveEndClippedReadFilter 2022-04-13T20:13:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5358809263643-WellformedReadFilter 2022-04-13T20:17:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5358809293339-SampleReadFilter 2022-04-13T20:13:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358809618715-PathSeqPipelineSpark 2022-04-22T17:40:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5358809710235-SecondOfPairReadFilter 2022-04-13T20:13:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358809795739-AS-StrandOddsRatio 2022-04-13T20:13:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358809892251-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2022-04-13T20:17:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5358810031643-RnaSeqMetrics 2022-04-13T20:13:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5358810375579-PrintReadsHeader 2022-04-13T20:17:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5358810425627-AnnotateVcfWithExpectedAlleleFraction 2022-04-13T20:17:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5358815637403-NonChimericOriginalAlignmentReadFilter 2022-04-13T20:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5358816130587-AnalyzeCovariates 2022-04-13T20:17:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358817095067-IlluminaBasecallingMetrics 2022-04-13T20:13:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358817193115-JumpingLibraryMetrics 2022-04-13T20:13:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5358817454875-CountVariants 2022-04-13T20:17:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5358817837979-FilterSamReads-Picard 2022-04-13T20:18:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5358818084251-StrandOddsRatio 2022-04-13T20:14:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5358818406043-DetermineGermlineContigPloidy 2022-04-13T20:14:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5358818483099-FindBreakpointEvidenceSpark-BETA 2022-04-13T20:18:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5358821936795-LibraryReadFilter 2022-04-13T20:13:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5358822321435-BarcodeMetric 2022-04-13T20:13:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5358822652315-CollectQualityYieldMetrics-Picard 2022-04-13T20:13:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5358822965531-FilterVcf-Picard 2022-04-13T20:13:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5358823087003-GcBiasSummaryMetrics 2022-04-13T20:13:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358823215643-CountReads 2022-04-13T20:17:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358823252251-FixVcfHeader-Picard 2022-04-13T20:17:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5358823682203-AllowAllReadsReadFilter 2022-04-13T20:13:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5358823768219-NotDuplicateReadFilter 2022-04-13T20:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358823847707-BamToBfq-Picard 2022-04-13T20:13:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5358823987099-VariantAnnotator 2022-09-19T20:48:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5358824205723-CountBases 2022-04-13T20:18:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358824293659--Tool-Documentation-Index 2022-04-13T20:18:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5358824485147-HasReadGroupReadFilter 2022-04-13T20:14:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5358825150107-CountVariantsSpark 2022-04-13T20:14:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5358825282331-SamFormatConverter-Picard 2022-04-13T20:14:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5358825808027-CalculateReadGroupChecksum-Picard 2022-04-13T20:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358826157723-CalculateFingerprintMetrics-Picard 2022-04-13T20:14:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358826263323-BwaSpark-BETA 2022-04-13T20:18:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5358826311835-CollectAlignmentSummaryMetrics-Picard 2022-04-13T20:14:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5358826431003-GenotypeConcordanceContingencyMetrics 2022-04-13T20:14:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358826654875-ApplyBQSR 2022-04-13T20:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358827078043-MappingQualityRankSumTest 2022-04-13T20:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358827306395-HsMetrics 2022-04-13T20:14:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5358829648283-GenotypeConcordance-Picard 2022-04-13T20:17:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358830093339-RMSMappingQuality 2022-04-13T20:13:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358830161051-FirstOfPairReadFilter 2022-04-13T20:13:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5358830252187-Funcotator 2022-09-20T13:16:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5358830948123-CollectHsMetrics-Picard 2022-04-13T20:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358831005339-AccumulateQualityYieldMetrics-Picard 2022-04-13T20:13:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358831085851-GnarlyGenotyper-BETA 2022-04-13T20:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5358831312027-ErrorMetric 2022-04-13T20:13:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358831835803-CollectMultipleMetricsSpark-BETA 2022-04-13T20:18:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5358832431131-VariantsToTable 2022-04-13T20:18:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5358832781467-UpdateVCFSequenceDictionary 2022-04-13T20:18:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358832960539-FisherStrand 2022-04-13T20:14:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5358833182491-SoftClippedReadFilter 2022-04-13T20:14:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358833264411-MarkDuplicatesSpark 2023-08-28T15:22:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5358833392539-SetNmMdAndUqTags-Picard 2022-04-13T20:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358833658907-BaitBiasSummaryMetrics 2022-04-13T20:14:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5358833829659-SamComparisonMetric 2022-04-13T20:14:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5358834032923-GatherVcfs-Picard 2022-04-13T20:14:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358834623515-InsertSizeMetrics 2022-12-30T08:14:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358834993307-MateDifferentStrandReadFilter 2022-04-13T20:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5358835082779-FilterMutectCalls 2022-04-13T20:18:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358835130523-FingerprintMetrics 2022-04-13T20:14:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5358835338139-AccumulateVariantCallingMetrics-Picard 2022-04-13T20:14:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5358835539611-CollectQualityYieldMetricsSpark-BETA 2022-04-13T20:18:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5358835573019-PlatformUnitReadFilter 2022-04-13T20:15:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5358837081371-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2022-04-13T20:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5358837279259-Pileup 2022-04-13T20:17:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358837389467-VerifyIDIntensityContaminationMetrics 2022-04-13T20:13:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5358838034971-AlignmentAgreesWithHeaderReadFilter 2022-04-13T20:13:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358838684187-EstimateLibraryComplexity-Picard 2022-04-13T20:13:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358838774427-ViewSam-Picard 2022-04-13T20:17:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5358839364251-PrimaryLineReadFilter 2022-04-13T20:14:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5358839656347-MendelianViolationMetrics 2022-04-13T20:14:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358840021403-UniqueAltReadCount 2022-04-13T20:14:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5358840083995-QualByDepth 2022-04-13T20:14:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5358840134555-NormalizeFasta-Picard 2022-04-13T20:18:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5358840289691-PFFailSummaryMetric 2022-04-13T20:14:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358840869915-ClusterCrosscheckMetrics-Picard 2022-04-13T20:14:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358841078299-GetSampleName 2022-04-13T20:18:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5358841858587-AnnotateVcfWithBamDepth 2022-04-13T20:18:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5358842355227-MakeSitesOnlyVcf-Picard 2022-04-13T20:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5358842397723-IntervalListTools-Picard 2022-04-13T20:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5358842547611-FragmentDepthPerAlleleBySample 2022-04-13T20:14:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358842698779-SortSamSpark-BETA 2022-04-13T20:18:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5358842762779-FilterIntervals 2022-04-13T20:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358842892059-HaplotypeCallerSpark-BETA 2022-04-13T20:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5358844096795-MateDistantReadFilter 2022-04-13T20:18:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358844339483-ChromosomeCounts 2022-04-13T20:13:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5358844727067-OverclippedReadFilter 2022-04-13T20:13:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358844768283-BwaMemIndexImageCreator 2022-04-13T20:17:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358844841755-NotProperlyPairedReadFilter 2022-04-13T20:13:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5358845395611-CalcMetadataSpark-BETA 2022-04-13T20:17:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358845652507-VariantEval-BETA 2022-04-13T20:13:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358846540571-VariantCallingSummaryMetrics 2022-04-13T20:13:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5358846608795-ArraysControlCodesSummaryMetrics 2022-04-13T20:13:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5358846717211-MergePedIntoVcf-Picard 2022-04-13T20:13:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5358847057691-CheckFingerprint-Picard 2022-04-13T20:14:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5358847359771-MappingQuality 2022-04-13T20:14:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5358847500699-AS-RMSMappingQuality 2022-04-13T20:14:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5358847661467-CNNVariantWriteTensors-EXPERIMENTAL 2022-04-13T20:18:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5358848644251-FuncotateSegments-BETA 2022-04-13T20:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5358848717595-GatherBamFiles-Picard 2022-04-13T20:14:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358849075867-CollectSequencingArtifactMetrics-Picard 2022-04-13T20:14:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358849291419-GatherBQSRReports 2022-04-13T20:14:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5358849412379-PathSeqBuildKmers 2022-04-13T20:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358849506459-CollectInsertSizeMetrics-Picard 2022-04-13T20:14:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5358849639195-CollectReadCounts 2022-04-13T20:18:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5358850221211-BaitBiasDetailMetrics 2022-04-13T20:14:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5358850256923-CalculateMixingFractions 2022-04-13T20:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358851293723-ReplaceSamHeader-Picard 2022-04-13T20:18:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358852071451-CheckIlluminaDirectory-Picard 2022-04-13T20:18:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5358852329371-ReblockGVCF 2022-04-13T20:18:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5358852436763-MergeBamAlignment-Picard 2022-04-13T20:15:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5358852561051-LiftOverIntervalList-Picard 2022-04-13T20:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358852631451-OverlappingErrorMetric 2022-04-13T20:13:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5358852758043-PreAdapterSummaryMetrics 2022-04-13T20:13:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5358852975387-BafRegressMetrics 2022-04-13T20:14:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5358854479003-ClipReads 2022-04-13T20:18:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5358854528539-CollectSamErrorMetrics-Picard 2022-04-13T20:14:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5358854704411-DepthPerAlleleBySample 2022-04-13T20:14:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5358854842395-GcBiasMetrics 2022-04-13T20:14:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5358854905755-CompareMetrics-Picard 2022-04-13T20:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5358855141403-AS-FisherStrand 2022-04-13T20:14:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358855168539-CompareBaseQualities 2022-04-13T20:14:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358855396251-MappedReadFilter 2022-04-13T20:14:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358855464731-MarkDuplicatesWithMateCigar-Picard 2022-04-13T20:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5358855608859-CpxVariantReInterpreterSpark-BETA 2022-04-13T20:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856018459-MappingQualityNotZeroReadFilter 2022-04-13T20:14:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856062747-GetNormalArtifactData 2022-04-13T20:18:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856144155-CollectJumpingLibraryMetrics-Picard 2022-04-13T20:14:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856188443-SplitSamByNumberOfReads-Picard 2022-04-13T20:18:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856254619-ComposeSTRTableFile 2022-04-13T20:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856605339-SelectVariants 2022-04-13T20:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856767259-ReadGroupReadFilter 2022-04-13T20:14:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5358856805403-MappingQualityReadFilter 2022-04-13T20:18:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358857328667-AlignmentSummaryMetrics 2022-04-13T20:15:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5358857932315-PathSeqBwaSpark 2022-04-13T20:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5358858010779-SampleList 2022-04-13T20:15:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5358858421019-CollectBaseDistributionByCycle-Picard 2022-04-13T20:15:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358858628507-RrbsCpgDetailMetrics 2022-04-13T20:15:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5358858922779-FeaturizedReadSets 2022-04-13T20:15:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358858953243-DuplicationMetrics 2022-04-13T20:15:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358859205275-BedToIntervalList-Picard 2022-04-13T20:19:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5358859364507-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2022-04-13T20:19:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358859678875-PreAdapterDetailMetrics 2022-04-13T20:15:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358859726235-ReorderSam-Picard 2022-04-13T20:15:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358859750811-RawWgsMetrics 2022-04-13T20:15:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358860059547-UmiMetrics 2022-04-13T20:15:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358860217115-GetPileupSummaries 2022-04-13T20:19:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5358860680987-DownsampleSam-Picard 2022-04-13T20:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5358860841371-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-04-13T20:19:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5358861112603-IlluminaBasecallsToFastq-Picard 2022-04-13T20:14:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5358861221659-PostProcessReadsForRSEM-BETA 2022-04-13T20:18:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5358861321243-GeneExpressionEvaluation-BETA 2022-04-13T20:18:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5358862160027-PathSeqBuildReferenceTaxonomy 2022-04-13T20:14:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358862585371-ExtractSequences-Picard 2022-04-13T20:18:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358862712347-CalculateContamination 2022-04-13T20:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5358863047579-StrandBiasBySample 2022-04-13T20:14:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358863119131-LearnReadOrientationModel 2022-04-13T20:14:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358863276443-LeftAlignIndels 2022-04-13T20:18:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358863710363-NonNFastaSize-Picard 2022-04-13T20:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5358864110235-IlluminaBasecallsToSam-Picard 2022-04-13T20:14:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5358864426011-CreateBafRegressMetricsFile-Picard 2022-04-13T20:15:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5358864465435-CreateHadoopBamSplittingIndex-BETA 2022-04-13T20:15:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller 2022-04-13T20:18:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358865227291-MateUnmappedAndUnmappedReadFilter 2022-04-13T20:15:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5358865313179-CountBasesInReference 2022-04-13T20:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5358865633435-MatchingBasesAndQualsReadFilter 2022-04-13T20:15:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5358865805467-FragmentLength 2022-04-13T20:15:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358866974107-OriginalAlignment 2022-04-13T20:15:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358867096859-GoodCigarReadFilter 2022-04-13T20:15:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5358867598235-CollectWgsMetrics-Picard 2022-04-13T20:15:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358868279835-GenotypeConcordanceDetailMetrics 2022-04-13T20:15:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358868574747-ArraysVariantCallingDetailMetrics 2022-04-13T20:15:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358868598299-TransferReadTags-EXPERIMENTAL 2023-06-07T13:22:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358868757275-BaseQualityRankSumTest 2022-04-13T20:15:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5358869471771-BaseRecalibratorSpark-BETA 2022-04-13T20:18:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358869751067-SVCluster-BETA 2022-04-13T20:18:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358869876891-GenomicsDBImport 2023-12-07T20:03:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5358870054427-PrintReads 2022-04-13T20:18:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5358870098843-GenotypeConcordanceSummaryMetrics 2022-04-13T20:15:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358870153499-BwaAndMarkDuplicatesPipelineSpark-BETA 2022-04-13T20:18:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358870913179-SetNmAndUqTags-Picard 2022-04-13T20:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358871024027-MarkIlluminaAdapters-Picard 2022-04-13T20:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5358871784475-FixMisencodedBaseQualityReads 2022-04-13T20:18:58Z https://gatk.broadinstitute.org/hc/en-us/articles/5358872248347-RemoveNearbyIndels 2022-04-13T20:19:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5358872471963-CreateSequenceDictionary-Picard 2022-04-13T20:19:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5358872755483-PostprocessGermlineCNVCalls 2022-04-13T20:19:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5358872775579-NotSupplementaryAlignmentReadFilter 2022-04-13T20:15:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358872824987-GenotypeSummaries 2022-04-13T20:15:41Z https://gatk.broadinstitute.org/hc/en-us/articles/5358872850587-FlagStatSpark 2022-04-13T20:19:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358873116827-AS-ReadPosRankSumTest 2022-04-13T20:15:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5358873269019-ExcessHet 2022-04-13T20:15:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358873312539-VariantFiltration 2023-07-07T14:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358873625755-ClippingRankSumTest 2022-04-13T20:15:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5358873893787-CollectInsertSizeMetricsSpark-BETA 2022-04-13T20:19:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358874158235-GermlineCNVCaller 2022-04-13T20:16:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5358874308635-ErrorSummaryMetrics 2022-04-13T20:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5358874331931-CallCopyRatioSegments 2022-04-13T20:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358874555931-IlluminaLaneMetrics 2022-04-13T20:16:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5358875253147-LiftoverVcf-Picard 2022-04-13T20:19:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358875408923-MateOnSameContigOrNoMappedMateReadFilter 2022-04-13T20:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358875572763-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2022-04-13T20:16:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5358875696411-ValidateVariants 2022-04-13T20:19:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5358875749147-CollectAllelicCounts 2022-04-13T20:19:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358875867419-MethylationTypeCaller-EXPERIMENTAL 2022-04-13T20:19:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358876160923-ReadLengthEqualsCigarLengthReadFilter 2022-04-13T20:19:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358876555419-GcBiasDetailMetrics 2022-04-13T20:16:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358876585499-CollectIlluminaBasecallingMetrics-Picard 2022-04-13T20:16:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358876714779-CollectRnaSeqMetrics-Picard 2022-04-13T20:16:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5358876755611-AnnotateIntervals 2022-04-13T20:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5358876821275-RevertSam-Picard 2022-04-13T20:20:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5358877016859-NonZeroReferenceLengthAlignmentReadFilter 2022-04-13T20:16:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358877049883-CollectBaseDistributionByCycleSpark-BETA 2022-04-13T20:20:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358877116571-PathSeqFilterSpark 2022-04-13T20:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5358877443995-DepthOfCoverage-BETA 2022-04-13T20:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358878324251-CountFalsePositives-BETA 2022-04-13T20:18:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5358878405019-CollectIlluminaLaneMetrics-Picard 2022-04-13T20:15:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5358878545691-VcfToIntervalList-Picard 2022-04-13T20:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358878811931-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2022-04-13T20:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358879207579-RrbsSummaryMetrics 2022-04-13T20:15:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358879711259-RevertSamSpark-BETA 2022-04-13T20:19:00Z https://gatk.broadinstitute.org/hc/en-us/articles/5358879872795-AmbiguousBaseReadFilter 2022-04-13T20:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358880072987-CollectRawWgsMetrics-Picard 2022-04-13T20:19:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358880192027-MarkDuplicates-Picard 2022-04-13T20:15:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358880238875-VcfToAdpc-Picard 2022-04-13T20:15:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5358880308507-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-04-13T20:15:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5358880834075-PairedReadFilter 2022-04-13T20:15:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5358881255707-RevertBaseQualityScores 2022-04-13T20:19:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5358881480475-BQSRPipelineSpark-BETA 2022-04-13T20:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5358881824539-IntervalListToBed-Picard 2022-04-13T20:15:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5358881998875-ReadNameReadFilter 2022-04-13T20:16:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5358882030875-MappingQualityZero 2022-04-13T20:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5358882219803-PlatformReadFilter 2022-04-13T20:16:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5358882641051-VcfFormatConverter-Picard 2022-04-13T20:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5358883370011-MergeVcfs-Picard 2022-04-13T20:19:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358883621915-FingerprintingSummaryMetrics 2022-04-13T20:16:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358883795867-FlagStat 2022-04-13T20:19:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5358883834011-CombineGenotypingArrayVcfs-Picard 2022-04-13T20:19:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5358884278683-WgsMetrics 2022-04-13T20:16:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358884334747-SortSam-Picard 2022-04-13T20:19:57Z https://gatk.broadinstitute.org/hc/en-us/articles/5358884598555-GatherVcfsCloud-BETA 2022-04-13T20:16:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5358884655771-PathSeqScoreSpark 2022-04-13T20:20:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5358884764955-SplitReads 2022-04-13T20:20:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5358884828443-BaseQuality 2022-04-13T20:16:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5358885215131-EvaluateInfoFieldConcordance-BETA 2022-04-13T20:20:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5358885494811-CigarContainsNoNOperator 2022-04-13T20:17:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358885908891-AS-BaseQualityRankSumTest 2022-04-13T20:17:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5358886012443-BuildBamIndex-Picard 2022-04-13T20:20:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358886289947-ValidAlignmentStartReadFilter 2022-04-13T20:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5358886409883-ReadsPipelineSpark-BETA 2022-04-13T20:18:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358886720539-ClusteredCrosscheckMetric 2022-04-13T20:15:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358887097371-MeanQualityByCycleSpark-BETA 2022-04-13T20:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358887321755-CollectTargetedPcrMetrics-Picard 2022-04-13T20:18:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5358887757979-LeftAlignAndTrimVariants 2022-04-13T20:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5358888043803-ExtractIlluminaBarcodes-Picard 2022-04-13T20:15:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358888081691-PFFailDetailedMetric 2022-04-13T20:15:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358888613659-PositionBasedDownsampleSam-Picard 2022-04-13T20:15:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5358888786843-BaseDistributionByCycleMetrics 2022-04-13T20:15:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358888905371-FilterAlignmentArtifacts-EXPERIMENTAL 2022-04-13T20:19:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5358889246107-FifoBuffer-Picard 2022-04-13T20:15:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358889384091-LikelihoodRankSumTest 2022-04-13T20:15:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358889613339-GatherTranches-BETA 2022-04-13T20:15:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5358889705371-VariantCallingDetailMetrics 2022-04-13T20:15:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358889748379-CompareSAMs-Picard 2022-04-13T20:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5358890204187-ApplyVQSR 2022-04-13T20:19:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358890543387-ScatterIntervalsByNs-Picard 2022-04-13T20:19:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5358890722459-QualityYieldMetrics 2022-04-13T20:16:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5358890853915-BamIndexStats-Picard 2022-04-13T20:19:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358891439771-CombineGVCFs 2022-04-13T20:19:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358891622171-ArraysVariantCallingSummaryMetrics 2022-04-13T20:16:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5358891684379-ReadPosition 2022-04-13T20:16:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5358892763803-ValidateSamFile-Picard 2022-04-13T20:16:37Z https://gatk.broadinstitute.org/hc/en-us/articles/5358892793755-BpmToNormalizationManifestCsv-Picard 2022-04-13T20:19:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358892827419-IndependentReplicateMetric 2022-04-13T20:16:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358893070491-FuncotatorDataSourceDownloader 2022-04-13T20:16:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358893663131-PlotDenoisedCopyRatios 2022-04-13T20:16:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5358893779227-UnmarkDuplicates 2022-04-13T20:20:09Z https://gatk.broadinstitute.org/hc/en-us/articles/5358894366363-CrosscheckFingerprints-Picard 2022-04-13T20:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5358894584987-ModelSegments 2022-04-13T20:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5358895038363-CompareDuplicatesSpark-BETA 2022-04-13T20:19:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5358895340443-AllelePseudoDepth 2022-04-13T20:15:36Z https://gatk.broadinstitute.org/hc/en-us/articles/5358896138011-BaseRecalibrator 2022-04-13T20:19:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358896595867-PossibleDeNovo 2022-04-13T20:15:56Z https://gatk.broadinstitute.org/hc/en-us/articles/5358896688155-DenoiseReadCounts 2022-08-19T07:51:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5358896966299-UpdateVcfSequenceDictionary-Picard 2022-04-13T20:16:02Z https://gatk.broadinstitute.org/hc/en-us/articles/5358897522587-CollectArraysVariantCallingMetrics-Picard 2022-04-13T20:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898116379-AddOATag-Picard 2022-04-13T20:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898207643-Coverage 2022-04-13T20:16:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898241051-TargetedPcrMetrics 2022-04-13T20:16:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898266011-ApplyBQSRSpark-BETA 2022-04-13T20:19:42Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898440731-CollectMultipleMetrics-Picard 2022-04-13T20:19:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898588571-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2022-04-13T20:16:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898687515-PreprocessIntervals 2022-04-13T20:19:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898898715-IlluminaPhasingMetrics 2022-04-13T20:16:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358898996507-SortVcf-Picard 2022-04-13T20:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/5358899175195-FastqToSam-Picard 2022-04-13T20:19:55Z https://gatk.broadinstitute.org/hc/en-us/articles/5358899754779-ReadPosRankSumTest 2022-04-13T20:16:50Z https://gatk.broadinstitute.org/hc/en-us/articles/5358900178459-NonZeroFragmentLengthReadFilter 2022-04-13T20:17:01Z https://gatk.broadinstitute.org/hc/en-us/articles/5358900347675-ProperlyPairedReadFilter 2022-04-13T20:17:04Z https://gatk.broadinstitute.org/hc/en-us/articles/5358900593307-CNNVariantTrain-EXPERIMENTAL 2022-04-13T20:20:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5358901172891-IndexFeatureFile 2022-04-13T20:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358901729307-CountReadsSpark 2022-04-13T20:20:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5358903057947-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2022-04-13T20:19:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358903172379-PrintSVEvidence-EXPERIMENTAL 2022-04-13T20:19:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358903464091-AS-InbreedingCoeff 2022-04-13T20:16:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5358904056859-PlotModeledSegments 2022-04-13T20:16:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358904105243-CollectVariantCallingMetrics-Picard 2022-04-13T20:16:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358904645915-CalculateGenotypePosteriors 2022-04-13T20:19:43Z https://gatk.broadinstitute.org/hc/en-us/articles/5358904785819-ExtractSVEvidenceSpark-BETA 2022-04-13T20:19:45Z https://gatk.broadinstitute.org/hc/en-us/articles/5358904862107-CNNScoreVariants 2022-04-13T20:19:46Z https://gatk.broadinstitute.org/hc/en-us/articles/5358905028123-QualityScoreDistribution-Picard 2022-04-13T20:16:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5358905149723-BaitDesigner-Picard 2022-04-13T20:19:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5358905249947-FixMateInformation-Picard 2022-04-13T20:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/5358905318811-PrintVariantsSpark 2022-04-13T20:19:54Z https://gatk.broadinstitute.org/hc/en-us/articles/5358905666459-MergeSamFiles-Picard 2022-04-13T20:19:59Z https://gatk.broadinstitute.org/hc/en-us/articles/5358905846811-PassesVendorQualityCheckReadFilter 2022-04-13T20:16:48Z https://gatk.broadinstitute.org/hc/en-us/articles/5358905916827-AS-MappingQualityRankSumTest 2022-04-13T20:16:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator 2022-04-13T20:20:05Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906166043-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2022-04-13T20:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906400667-SplitNCigarReads 2022-04-13T20:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906515867-PileupSpark-BETA 2022-04-13T20:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906539291-BaseErrorMetric 2022-04-13T20:17:03Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906633883-SplitVcfs-Picard 2022-04-13T20:20:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906657179-FilterFuncotations-EXPERIMENTAL 2022-04-13T20:20:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906861083-GenotypeGVCFs 2022-04-13T20:20:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5358906970779-AnalyzeSaturationMutagenesis-BETA 2022-04-13T20:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907124763-CollectRrbsMetrics-Picard 2022-04-13T20:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907205659-WgsMetricsWithNonZeroCoverage 2022-04-13T20:17:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907263515-ShiftFasta-BETA 2022-04-13T20:20:23Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907341467-MetricsReadFilter 2022-04-13T20:17:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907383323-ValidAlignmentEndReadFilter 2022-04-13T20:20:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907571483-ConvertSequencingArtifactToOxoG-Picard 2022-04-13T20:17:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907615387-OrientationBiasReadCounts 2022-04-13T20:17:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907662235-AssemblyComplexity 2022-04-13T20:17:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907790235-CollectOxoGMetrics-Picard 2022-04-13T20:17:30Z https://gatk.broadinstitute.org/hc/en-us/articles/5358907823259-CreateReadCountPanelOfNormals 2022-09-07T19:40:21Z https://gatk.broadinstitute.org/hc/en-us/articles/5358908102043-CheckPileup 2022-04-13T20:20:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358908206491-ReadLengthReadFilter 2022-04-13T20:17:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358908234651-CleanSam-Picard 2022-04-13T20:17:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2 2022-04-13T20:19:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358911744027-TargetMetrics 2022-04-13T20:16:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5358911906459-AddOrReplaceReadGroups-Picard 2022-04-13T20:16:12Z https://gatk.broadinstitute.org/hc/en-us/articles/5358912067611-TheoreticalSensitivityMetrics 2022-04-13T20:16:14Z https://gatk.broadinstitute.org/hc/en-us/articles/5358912149275-LocalAssembler-BETA 2022-04-13T20:19:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358912200347-CollectGcBiasMetrics-Picard 2022-09-29T13:45:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5358912446107-ReadStrandFilter 2022-04-13T20:16:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5358912868379-CpcgMetrics 2022-04-13T20:16:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358913020955-PrintDistantMates 2022-04-13T20:19:49Z https://gatk.broadinstitute.org/hc/en-us/articles/5358913184923-InbreedingCoeff 2022-04-13T20:16:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358913499803-ReadGroupBlackListReadFilter 2022-04-13T20:16:39Z https://gatk.broadinstitute.org/hc/en-us/articles/5358913555099-SamToFastq-Picard 2022-07-24T15:58:47Z https://gatk.broadinstitute.org/hc/en-us/articles/5358913715099-ConvertHeaderlessHadoopBamShardToBam-BETA 2022-04-13T20:16:44Z https://gatk.broadinstitute.org/hc/en-us/articles/5358914088347-SeqIsStoredReadFilter 2022-04-13T20:16:51Z https://gatk.broadinstitute.org/hc/en-us/articles/5358914109851-IntervalOverlapReadFilter 2022-04-13T20:16:52Z https://gatk.broadinstitute.org/hc/en-us/articles/5358914364699-SplitIntervals 2022-04-13T20:20:07Z https://gatk.broadinstitute.org/hc/en-us/articles/5358914434331-FastaAlternateReferenceMaker 2022-04-13T20:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/5358914532891-StructuralVariationDiscoveryPipelineSpark-BETA 2022-04-13T20:20:10Z https://gatk.broadinstitute.org/hc/en-us/articles/5358914984987-SplitSamByLibrary-Picard 2022-04-13T20:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/5358915293083-FindBadGenomicKmersSpark-BETA 2022-04-13T20:20:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5358915594907-NotSecondaryAlignmentReadFilter 2022-04-13T20:17:17Z https://gatk.broadinstitute.org/hc/en-us/articles/5358915683611-IndelErrorMetric 2022-04-13T20:17:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358915861787-FingerprintingDetailMetrics 2022-04-13T20:17:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5358916449563-PrintReadsSpark 2022-04-13T20:20:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5358920001563-FragmentLengthReadFilter 2022-04-13T20:17:15Z https://gatk.broadinstitute.org/hc/en-us/articles/5358920140059-FindMendelianViolations-Picard 2022-04-13T20:20:22Z https://gatk.broadinstitute.org/hc/en-us/articles/5358920441243-QualityScoreDistributionSpark-BETA 2022-04-13T20:20:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358920647835-CountNs 2022-04-13T20:17:27Z https://gatk.broadinstitute.org/hc/en-us/articles/5358920677403-RenameSampleInVcf-Picard 2022-04-13T20:20:28Z https://gatk.broadinstitute.org/hc/en-us/articles/5358920709531-ReadAnonymizer-EXPERIMENTAL 2022-04-13T20:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358920917787-ASEReadCounter 2022-04-13T20:20:32Z https://gatk.broadinstitute.org/hc/en-us/articles/5358921041947-CreateSomaticPanelOfNormals-BETA 2022-04-13T20:20:34Z https://gatk.broadinstitute.org/hc/en-us/articles/5358921146907-CheckTerminatorBlock-Picard 2022-04-13T20:17:38Z https://gatk.broadinstitute.org/hc/en-us/articles/5358928298523-FastaReferenceMaker 2022-04-13T20:20:26Z https://gatk.broadinstitute.org/hc/en-us/articles/5358928423067-AlleleFraction 2022-04-13T20:17:25Z https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches 2022-04-13T20:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358936519579-TandemRepeat 2022-04-13T20:17:11Z https://gatk.broadinstitute.org/hc/en-us/articles/5358936573723-AddCommentsToBam-Picard 2022-04-13T20:20:18Z https://gatk.broadinstitute.org/hc/en-us/articles/5358936645275-AS-QualByDepth 2022-04-13T20:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/5358936704667-Concordance 2022-04-13T20:20:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5358937000219-ReferenceBases 2022-04-13T20:17:20Z https://gatk.broadinstitute.org/hc/en-us/articles/5358937249307-DepthPerSampleHC 2022-04-13T20:17:24Z https://gatk.broadinstitute.org/hc/en-us/articles/5358937508251-MappingQualityAvailableReadFilter 2022-04-13T20:17:29Z https://gatk.broadinstitute.org/hc/en-us/articles/5358937621787-CollectDuplicateMetrics-Picard 2022-04-13T20:17:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5358937676571-CountBasesSpark 2022-04-13T20:20:31Z https://gatk.broadinstitute.org/hc/en-us/articles/5358937811483-CalibrateDragstrModel 2022-04-13T20:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/5358937954203-GtcToVcf-Picard 2022-04-13T20:17:37Z https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot-obsolete-as-of-GATK-4-6-0-0 2024-07-01T17:16:54Z https://gatk.broadinstitute.org/hc/en-us/articles/6355692091547-GATK-on-IBM-Cloud 2024-06-25T07:17:23Z https://gatk.broadinstitute.org/hc/en-us/articles/8516241685787-Hacking-GATK-to-reduce-your-cloud-costs 2024-07-01T17:07:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9022476791323-Structural-Variants 2025-01-03T12:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9022487952155-Structural-variant-SV-discovery 2024-07-08T19:41:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9022653744283-GATK-Best-Practices-for-Structural-Variation-Discovery-on-Single-Samples 2024-07-08T19:38:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9434799593243--DRAGEN-GATK-Webinar-Oct-21-2022 2024-07-08T20:08:39Z https://gatk.broadinstitute.org/hc/en-us/articles/9570209965083-NonChimericOriginalAlignmentReadFilter 2022-10-13T14:10:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570210353563-Pileup 2022-10-13T14:17:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570225682843-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2022-10-13T14:17:34Z https://gatk.broadinstitute.org/hc/en-us/articles/9570226812443-OverclippedReadFilter 2022-10-13T14:10:43Z https://gatk.broadinstitute.org/hc/en-us/articles/9570226904091-BwaMemIndexImageCreator 2022-10-13T14:17:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570232354331-MeanQualityByCycle-Picard 2022-10-13T14:17:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570233252123-BarcodeMetric 2022-10-13T14:10:48Z https://gatk.broadinstitute.org/hc/en-us/articles/9570233538971-AnalyzeCovariates 2022-10-13T14:17:44Z https://gatk.broadinstitute.org/hc/en-us/articles/9570234210075-PathSeqPipelineSpark 2022-10-13T14:17:49Z https://gatk.broadinstitute.org/hc/en-us/articles/9570234341147-CalcMetadataSpark-BETA 2022-10-13T14:17:49Z https://gatk.broadinstitute.org/hc/en-us/articles/9570241433883-CollectHiSeqXPfFailMetrics-Picard 2022-10-13T14:10:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570241520795-GenotypeConcordance-Picard 2022-10-13T14:17:39Z https://gatk.broadinstitute.org/hc/en-us/articles/9570242174235-ExcessiveEndClippedReadFilter 2022-10-13T14:10:47Z https://gatk.broadinstitute.org/hc/en-us/articles/9570243570459-AS-StrandOddsRatio 2022-10-13T14:11:00Z https://gatk.broadinstitute.org/hc/en-us/articles/9570243836187-VariantEval-BETA 2025-09-30T15:51:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570246700315-LibraryReadFilter 2022-10-13T14:10:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570248460699-RMSMappingQuality 2022-10-13T14:10:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570248865691-CollectQualityYieldMetrics-Picard 2022-10-13T14:10:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570249292315-AlignmentAgreesWithHeaderReadFilter 2022-10-13T14:10:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570249478555-FilterVcf-Picard 2022-10-13T14:11:00Z https://gatk.broadinstitute.org/hc/en-us/articles/9570249761307-GcBiasSummaryMetrics 2022-10-13T14:11:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570250692379-JumpingLibraryMetrics 2022-10-13T14:11:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570256802587-ChromosomeCounts 2022-10-13T14:10:34Z https://gatk.broadinstitute.org/hc/en-us/articles/9570257027995-DumpTabixIndex 2022-10-13T14:10:36Z https://gatk.broadinstitute.org/hc/en-us/articles/9570257136155-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2022-10-13T14:10:37Z https://gatk.broadinstitute.org/hc/en-us/articles/9570257919515-VerifyIDIntensityContaminationMetrics 2022-10-13T14:10:45Z https://gatk.broadinstitute.org/hc/en-us/articles/9570258300187-WellformedReadFilter 2022-10-13T14:17:43Z https://gatk.broadinstitute.org/hc/en-us/articles/9570259312923-SecondOfPairReadFilter 2022-10-13T14:10:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570259666715-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2022-10-13T14:17:52Z https://gatk.broadinstitute.org/hc/en-us/articles/9570260035227-RnaSeqMetrics 2022-10-13T14:11:04Z https://gatk.broadinstitute.org/hc/en-us/articles/9570261021467-NotProperlyPairedReadFilter 2022-10-13T14:10:45Z https://gatk.broadinstitute.org/hc/en-us/articles/9570261743131-FirstOfPairReadFilter 2022-10-13T14:10:52Z https://gatk.broadinstitute.org/hc/en-us/articles/9570261939355-Funcotator 2022-10-13T14:17:46Z https://gatk.broadinstitute.org/hc/en-us/articles/9570263959067-GnarlyGenotyper-BETA 2022-10-13T14:17:57Z https://gatk.broadinstitute.org/hc/en-us/articles/9570264328603-EstimateLibraryComplexity-Picard 2022-10-13T14:11:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570264739995-ErrorMetric 2022-10-13T14:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/9570265420059-OverlappingErrorMetric 2022-10-13T14:11:24Z https://gatk.broadinstitute.org/hc/en-us/articles/9570266367899-BafRegressMetrics 2022-10-13T14:11:32Z https://gatk.broadinstitute.org/hc/en-us/articles/9570266920219--Tool-Documentation-Index 2022-10-13T14:18:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570268630683-IlluminaBasecallsToFastq-Picard 2022-10-13T14:11:56Z https://gatk.broadinstitute.org/hc/en-us/articles/9570269127451-ClusterCrosscheckMetrics-Picard 2022-10-13T14:12:00Z https://gatk.broadinstitute.org/hc/en-us/articles/9570269336219-IlluminaBasecallingMetrics 2022-10-13T14:11:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570270300955-AnnotateVcfWithExpectedAlleleFraction 2022-10-13T14:18:01Z https://gatk.broadinstitute.org/hc/en-us/articles/9570270598811-CountVariants 2022-10-13T14:18:02Z https://gatk.broadinstitute.org/hc/en-us/articles/9570271608219-VariantAnnotator 2022-10-13T14:18:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570271804571-MergePedIntoVcf-Picard 2022-10-13T14:11:30Z https://gatk.broadinstitute.org/hc/en-us/articles/9570272224027-CompareReferences-EXPERIMENTAL 2022-10-13T14:18:11Z https://gatk.broadinstitute.org/hc/en-us/articles/9570272820379-HasReadGroupReadFilter 2022-10-13T14:11:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570273799835-NormalizeFasta-Picard 2022-10-13T14:18:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570274300187-UpdateVCFSequenceDictionary 2022-10-13T14:18:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570274797339-GeneExpressionEvaluation-BETA 2022-10-13T14:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/9570275468059-SiteDepthtoBAF-EXPERIMENTAL 2022-10-13T14:18:36Z https://gatk.broadinstitute.org/hc/en-us/articles/9570275954331-SetNmMdAndUqTags-Picard 2022-10-13T14:18:39Z https://gatk.broadinstitute.org/hc/en-us/articles/9570276260635-FuncotateSegments-BETA 2022-10-13T14:18:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570276372635-GatherBamFiles-Picard 2022-10-13T14:12:15Z https://gatk.broadinstitute.org/hc/en-us/articles/9570277388699-AnnotateVcfWithBamDepth 2022-10-13T14:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/9570277818651-SampleReadFilter 2022-10-13T14:10:50Z https://gatk.broadinstitute.org/hc/en-us/articles/9570279665435-CountReads 2022-10-13T14:17:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570279810075-FixVcfHeader-Picard 2022-10-13T14:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570279989019-AccumulateQualityYieldMetrics-Picard 2022-10-13T14:11:09Z https://gatk.broadinstitute.org/hc/en-us/articles/9570280853787-ViewSam-Picard 2022-10-13T14:18:00Z https://gatk.broadinstitute.org/hc/en-us/articles/9570281877019-BamToBfq-Picard 2022-10-13T14:11:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570282075163-PreAdapterSummaryMetrics 2022-10-13T14:11:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570282156443-ArraysControlCodesSummaryMetrics 2022-10-13T14:11:28Z https://gatk.broadinstitute.org/hc/en-us/articles/9570282347419-FilterSamReads-Picard 2022-10-13T14:18:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570283085083-StrandOddsRatio 2022-10-13T14:11:37Z https://gatk.broadinstitute.org/hc/en-us/articles/9570283311515-MendelianViolationMetrics 2022-10-13T14:11:39Z https://gatk.broadinstitute.org/hc/en-us/articles/9570283748379-UniqueAltReadCount 2022-10-13T14:11:44Z https://gatk.broadinstitute.org/hc/en-us/articles/9570283814939-MappingQuality 2022-10-13T14:11:44Z https://gatk.broadinstitute.org/hc/en-us/articles/9570284085275-FlowBasedTPAttributeSymetricReadFilter 2022-10-13T14:11:47Z https://gatk.broadinstitute.org/hc/en-us/articles/9570284189723-VariantsToTable 2022-10-13T14:18:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570285767067-SoftClippedReadFilter 2023-02-20T11:47:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570285873691-GetSampleName 2022-10-13T14:18:34Z https://gatk.broadinstitute.org/hc/en-us/articles/9570286000539-CollectSVEvidence-BETA 2022-10-13T14:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570287342619-FindBreakpointEvidenceSpark-BETA 2022-10-13T14:18:18Z https://gatk.broadinstitute.org/hc/en-us/articles/9570287678235-FlowFeatureMapper-EXPERIMENTAL 2022-10-13T14:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570288755995-SamFormatConverter-Picard 2022-10-13T14:11:57Z https://gatk.broadinstitute.org/hc/en-us/articles/9570288863387-PostProcessReadsForRSEM-BETA 2022-10-13T14:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570288968347-FisherStrand 2022-10-13T14:11:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570290428443-GcBiasMetrics 2022-10-13T14:12:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570291238171-CompareBaseQualities 2022-10-13T14:12:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570292242587-MarkDuplicatesWithMateCigar-Picard 2022-10-13T14:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570292625051-CpxVariantReInterpreterSpark-BETA 2022-10-13T14:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570293421723-CollectReadCounts 2022-10-13T14:18:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570294185243-MappingQualityNotZeroReadFilter 2022-10-13T14:12:48Z https://gatk.broadinstitute.org/hc/en-us/articles/9570294813979-CollectHsMetrics-Picard 2022-10-13T14:17:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570295630747-PrintReadsHeader 2022-10-13T14:17:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570296190235-AllowAllReadsReadFilter 2022-10-13T14:11:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570296325403-LiftOverIntervalList-Picard 2022-10-13T14:11:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570296493467-NotDuplicateReadFilter 2022-10-13T14:11:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570296801179-VariantCallingSummaryMetrics 2022-10-13T14:11:26Z https://gatk.broadinstitute.org/hc/en-us/articles/9570297817883-CountBases 2022-10-13T14:18:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570298419611-DetermineGermlineContigPloidy 2023-03-04T04:19:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570298795931-QualByDepth 2022-10-13T14:11:45Z https://gatk.broadinstitute.org/hc/en-us/articles/9570299781659-CountVariantsSpark 2022-10-13T14:11:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570300724763-ReadGroupHasFlowOrderReadFilter 2022-10-13T14:12:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570301382555-HaplotypeFilteringAnnotation 2022-10-13T14:12:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570301646235-CompareMetrics-Picard 2022-10-13T14:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570302913819-CollectSamErrorMetrics-Picard 2022-10-13T14:12:02Z https://gatk.broadinstitute.org/hc/en-us/articles/9570303528603-DepthPerAlleleBySample 2023-02-11T23:21:22Z https://gatk.broadinstitute.org/hc/en-us/articles/9570304475675-PathSeqBuildReferenceTaxonomy 2022-10-13T14:12:18Z https://gatk.broadinstitute.org/hc/en-us/articles/9570304567963-AS-FisherStrand 2022-10-13T14:12:19Z https://gatk.broadinstitute.org/hc/en-us/articles/9570304800667-BwaSpark-BETA 2022-10-13T14:18:45Z https://gatk.broadinstitute.org/hc/en-us/articles/9570304897179-SamComparisonMetric 2022-10-13T14:12:22Z https://gatk.broadinstitute.org/hc/en-us/articles/9570305020059-CollectAlignmentSummaryMetrics-Picard 2022-10-13T14:12:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570305815195-GatherBQSRReports 2022-10-13T14:12:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570307105179-InsertSizeMetrics 2022-10-13T14:12:43Z https://gatk.broadinstitute.org/hc/en-us/articles/9570307622171-MappingQualityRankSumTest 2022-10-13T14:12:47Z https://gatk.broadinstitute.org/hc/en-us/articles/9570308092187-CollectJumpingLibraryMetrics-Picard 2022-10-13T14:12:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570308651931-ComposeSTRTableFile 2022-10-13T14:19:06Z https://gatk.broadinstitute.org/hc/en-us/articles/9570309302171-BaseRecalibratorSpark-BETA 2022-10-13T14:19:09Z https://gatk.broadinstitute.org/hc/en-us/articles/9570309492251-BaitBiasDetailMetrics 2022-10-13T14:13:01Z https://gatk.broadinstitute.org/hc/en-us/articles/9570310367643-ReadGroupReadFilter 2022-10-13T14:13:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570313292443-PrimaryLineReadFilter 2022-10-13T14:11:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570313568923-CollectMultipleMetricsSpark-BETA 2022-10-13T14:18:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570314191899-CheckFingerprint-Picard 2022-10-13T14:11:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570315228187-HaplotypeBasedVariantRecaller-EXPERIMENTAL 2022-10-13T14:18:22Z https://gatk.broadinstitute.org/hc/en-us/articles/9570315414683-AS-RMSMappingQuality 2022-10-13T14:11:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570315513755-PFFailSummaryMetric 2022-10-13T14:11:52Z https://gatk.broadinstitute.org/hc/en-us/articles/9570315581467-CNNVariantWriteTensors-EXPERIMENTAL 2022-10-13T14:18:24Z https://gatk.broadinstitute.org/hc/en-us/articles/9570316488475-ClipReads 2022-10-13T14:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570318058267-CalculateFingerprintMetrics-Picard 2022-10-13T14:12:17Z https://gatk.broadinstitute.org/hc/en-us/articles/9570319741083-MarkDuplicatesSpark 2022-10-13T14:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/9570319914139-CalculateReadGroupChecksum-Picard 2022-10-13T14:18:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570320613147-BaitBiasSummaryMetrics 2022-10-13T14:12:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570321726363-GenotypeConcordanceContingencyMetrics 2022-10-13T14:12:26Z https://gatk.broadinstitute.org/hc/en-us/articles/9570322072091-ExtractSequences-Picard 2022-10-13T14:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570322332315-CalculateContamination 2023-07-05T18:42:48Z https://gatk.broadinstitute.org/hc/en-us/articles/9570322958363-CollectInsertSizeMetrics-Picard 2022-10-13T14:12:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570323038107-StrandBiasBySample 2022-10-13T14:12:39Z https://gatk.broadinstitute.org/hc/en-us/articles/9570325044123-MateDifferentStrandReadFilter 2022-10-13T14:19:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570326304155-ScoreVariantAnnotations-BETA 2022-10-13T14:19:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570326648475-GenomicsDBImport 2022-10-13T14:19:15Z https://gatk.broadinstitute.org/hc/en-us/articles/9570326812187-PlatformUnitReadFilter 2022-10-13T14:13:11Z https://gatk.broadinstitute.org/hc/en-us/articles/9570326949403-RawGtCount 2022-10-13T14:13:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570327431451-BwaAndMarkDuplicatesPipelineSpark-BETA 2022-10-13T14:19:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570328153243-MappedReadFilter 2023-01-13T08:41:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570328871195-PathSeqBuildKmers 2022-10-13T14:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570329571227-LearnReadOrientationModel 2022-10-13T14:12:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570330067227-LeftAlignIndels 2022-10-13T14:19:00Z https://gatk.broadinstitute.org/hc/en-us/articles/9570330242203-FilterIntervals 2022-10-13T14:12:47Z https://gatk.broadinstitute.org/hc/en-us/articles/9570330546971-GetNormalArtifactData 2022-10-13T14:19:02Z https://gatk.broadinstitute.org/hc/en-us/articles/9570331605531-FilterMutectCalls 2022-10-13T14:19:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570332289307-SelectVariants 2023-03-14T15:04:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570332712219-SVCluster-BETA 2022-10-13T14:19:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570333562267-CollectQualityYieldMetricsSpark-BETA 2022-10-13T14:19:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570334998171-HaplotypeCaller 2022-10-13T14:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570335080731-AlignmentSummaryMetrics 2022-10-13T14:13:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570335178523-ValidAlignmentStartReadFilter 2022-10-13T14:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/9570335455131-ReplaceSamHeader-Picard 2022-10-13T14:19:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570336439451-CollectSequencingArtifactMetrics-Picard 2022-10-13T14:12:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570336657691-GatherVcfs-Picard 2022-10-13T14:12:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570337264923-ApplyBQSR 2022-10-13T14:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570340348059-FingerprintMetrics 2022-10-13T14:12:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570340746395-CalculateMixingFractions 2022-10-13T14:19:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570341001755-AccumulateVariantCallingMetrics-Picard 2022-10-13T14:13:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570342110363-CreateBafRegressMetricsFile-Picard 2022-10-13T14:13:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570343462043-ReadsPipelineSpark-BETA 2022-10-13T14:19:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570345080091-SplitSamByNumberOfReads-Picard 2022-10-13T14:19:05Z https://gatk.broadinstitute.org/hc/en-us/articles/9570345270555-HsMetrics 2022-10-13T14:12:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570346869403-IlluminaBasecallsToSam-Picard 2022-10-13T14:13:04Z https://gatk.broadinstitute.org/hc/en-us/articles/9570347441947-MappingQualityReadFilter 2022-10-13T14:19:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570348155291-CreateHadoopBamSplittingIndex-BETA 2022-10-13T14:13:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570348556443-HmerQualitySymetricReadFilter 2022-10-13T14:13:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570350919195-MatchingBasesAndQualsReadFilter 2022-10-13T14:13:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570351247643-FragmentLength 2022-10-13T14:13:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570352750875-PFFailDetailedMetric 2022-10-13T14:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570352934427-BedToIntervalList-Picard 2022-10-13T14:19:44Z https://gatk.broadinstitute.org/hc/en-us/articles/9570353036059-RemoveNearbyIndels 2022-10-13T14:19:45Z https://gatk.broadinstitute.org/hc/en-us/articles/9570353462299-MakeSitesOnlyVcf-Picard 2022-10-13T14:18:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570353641371-IntervalListTools-Picard 2022-10-13T14:18:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570354028187-FragmentDepthPerAlleleBySample 2022-10-13T14:12:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570354465435-SortSamSpark-BETA 2022-10-13T14:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570355342363-HaplotypeCallerSpark-BETA 2022-10-13T14:19:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570356113051-NonNFastaSize-Picard 2022-10-13T14:19:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570358532379-PrintReads 2022-10-13T14:19:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570358673435-GenotypeConcordanceSummaryMetrics 2022-10-13T14:13:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570359030939-MateDistantReadFilter 2022-10-13T14:19:22Z https://gatk.broadinstitute.org/hc/en-us/articles/9570362805275-CountFalsePositives-BETA 2022-10-13T14:19:26Z https://gatk.broadinstitute.org/hc/en-us/articles/9570363019931-MateUnmappedAndUnmappedReadFilter 2022-10-13T14:13:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570363302427-CountBasesInReference 2022-10-13T14:19:28Z https://gatk.broadinstitute.org/hc/en-us/articles/9570363431067-ClusteredCrosscheckMetric 2022-10-13T14:13:29Z https://gatk.broadinstitute.org/hc/en-us/articles/9570363868315-PathSeqBwaSpark 2023-02-12T12:26:05Z https://gatk.broadinstitute.org/hc/en-us/articles/9570365178779-RrbsCpgDetailMetrics 2022-10-13T14:13:44Z https://gatk.broadinstitute.org/hc/en-us/articles/9570365423259-MergeBamAlignment-Picard 2022-10-13T14:13:46Z https://gatk.broadinstitute.org/hc/en-us/articles/9570365713819-ModelSegments 2022-10-13T14:19:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570365867931-FeaturizedReadSets 2022-10-13T14:13:50Z https://gatk.broadinstitute.org/hc/en-us/articles/9570367651099-VcfToAdpc-Picard 2022-10-13T14:14:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570367951515-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-10-13T14:14:09Z https://gatk.broadinstitute.org/hc/en-us/articles/9570368136347-PositionBasedDownsampleSam-Picard 2022-10-13T14:14:11Z https://gatk.broadinstitute.org/hc/en-us/articles/9570368333339-PreAdapterDetailMetrics 2022-10-13T14:14:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570369946651-JexlExpressionReadTagValueFilter 2022-10-13T14:13:29Z https://gatk.broadinstitute.org/hc/en-us/articles/9570370700315-SampleList 2022-10-13T14:13:34Z https://gatk.broadinstitute.org/hc/en-us/articles/9570371126555-MeanQualityByCycleSpark-BETA 2022-10-13T14:19:33Z https://gatk.broadinstitute.org/hc/en-us/articles/9570371444635-CollectTargetedPcrMetrics-Picard 2022-10-13T14:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570371659419-RrbsSummaryMetrics 2022-10-13T14:13:42Z https://gatk.broadinstitute.org/hc/en-us/articles/9570371970587-TrainVariantAnnotationsModel-BETA 2022-10-13T14:19:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570372912667-ExtractIlluminaBarcodes-Picard 2022-10-13T14:13:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570373488667-CompareDuplicatesSpark-BETA 2022-10-13T14:19:45Z https://gatk.broadinstitute.org/hc/en-us/articles/9570375596315-GenotypeSummaries 2022-10-13T14:14:18Z https://gatk.broadinstitute.org/hc/en-us/articles/9570376040347-UmiMetrics 2022-10-13T14:14:22Z https://gatk.broadinstitute.org/hc/en-us/articles/9570376365467-FifoBuffer-Picard 2022-10-13T14:14:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570376731291-LikelihoodRankSumTest 2022-10-13T14:14:28Z https://gatk.broadinstitute.org/hc/en-us/articles/9570376886683-BaseRecalibrator 2022-10-13T14:20:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570378530075-CollectIlluminaLaneMetrics-Picard 2022-10-13T14:13:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570378820635-VcfToIntervalList-Picard 2022-10-13T14:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/9570378901019-SetNmAndUqTags-Picard 2022-10-13T14:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/9570379066395-MarkIlluminaAdapters-Picard 2022-10-13T14:19:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570379400091-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2022-10-13T14:19:33Z https://gatk.broadinstitute.org/hc/en-us/articles/9570381050907-AmbiguousBaseReadFilter 2022-10-13T14:13:56Z https://gatk.broadinstitute.org/hc/en-us/articles/9570381426971-CollectRawWgsMetrics-Picard 2022-10-13T14:19:46Z https://gatk.broadinstitute.org/hc/en-us/articles/9570381778587-MarkDuplicates-Picard 2022-10-13T14:14:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570384352283-ExcessHet 2022-10-13T14:14:26Z https://gatk.broadinstitute.org/hc/en-us/articles/9570384863131-RevertBaseQualityScores 2022-10-13T14:20:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570385574427-BQSRPipelineSpark-BETA 2022-10-13T14:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570387124251-OriginalAlignment 2022-10-13T14:14:02Z https://gatk.broadinstitute.org/hc/en-us/articles/9570388775195-NotSupplementaryAlignmentReadFilter 2022-10-13T14:14:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570388892699-BaseDistributionByCycleMetrics 2022-10-13T14:14:17Z https://gatk.broadinstitute.org/hc/en-us/articles/9570389354011-FilterAlignmentArtifacts-EXPERIMENTAL 2022-10-13T14:19:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570389458331-CollectWgsMetrics-Picard 2022-10-13T14:14:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570391725851-TransferReadTags-EXPERIMENTAL 2022-10-13T14:20:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570392395675-DenoiseReadCounts 2022-10-13T14:14:49Z https://gatk.broadinstitute.org/hc/en-us/articles/9570392740123-IntervalListToBed-Picard 2022-10-13T14:14:52Z https://gatk.broadinstitute.org/hc/en-us/articles/9570392914331-GermlineCNVCaller 2022-10-13T14:14:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570393016731-UpdateVcfSequenceDictionary-Picard 2022-10-13T14:14:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570393500443-CallCopyRatioSegments 2022-10-13T14:14:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570393863195-QualityYieldMetrics 2022-10-13T14:15:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570393950107-IlluminaLaneMetrics 2022-10-13T14:15:04Z https://gatk.broadinstitute.org/hc/en-us/articles/9570395825179-CheckIlluminaDirectory-Picard 2022-10-13T14:19:34Z https://gatk.broadinstitute.org/hc/en-us/articles/9570396018715-CollectBaseDistributionByCycle-Picard 2022-10-13T14:13:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570397946651-HmerIndelLength 2022-10-13T14:14:00Z https://gatk.broadinstitute.org/hc/en-us/articles/9570398017819-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2022-10-13T14:19:47Z https://gatk.broadinstitute.org/hc/en-us/articles/9570398685595-GoodCigarReadFilter 2022-10-13T14:14:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570399085467-CheckReferenceCompatibility-EXPERIMENTAL 2022-10-13T14:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570399261723-ReorderSam-Picard 2022-10-13T14:14:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570399360795-RawWgsMetrics 2022-10-13T14:14:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570399451035-PostprocessGermlineCNVCalls 2022-10-13T14:19:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570400229019-PairedReadFilter 2022-10-13T14:14:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570400320027-AS-ReadPosRankSumTest 2022-10-13T14:14:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570401232795-GatherTranches-BETA 2022-10-13T14:14:33Z https://gatk.broadinstitute.org/hc/en-us/articles/9570401673243-CompareSAMs-Picard 2022-10-13T14:20:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570402032411-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2022-10-13T14:20:09Z https://gatk.broadinstitute.org/hc/en-us/articles/9570402164251-ArraysVariantCallingDetailMetrics 2022-10-13T14:14:42Z https://gatk.broadinstitute.org/hc/en-us/articles/9570402516763-IndelClassify 2022-10-13T14:14:45Z https://gatk.broadinstitute.org/hc/en-us/articles/9570402909339-CollectInsertSizeMetricsSpark-BETA 2022-10-13T14:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570403488667-VariantFiltration 2024-01-03T21:00:19Z https://gatk.broadinstitute.org/hc/en-us/articles/9570407107739-AS-InbreedingCoeff 2022-10-13T14:15:01Z https://gatk.broadinstitute.org/hc/en-us/articles/9570407253659-PlatformReadFilter 2022-10-13T14:15:02Z https://gatk.broadinstitute.org/hc/en-us/articles/9570408150299-VariantType 2022-10-13T14:15:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570408226459-VcfFormatConverter-Picard 2022-10-13T14:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/9570408608539-CollectVariantCallingMetrics-Picard 2022-10-13T14:15:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570410550171-MergeVcfs-Picard 2022-10-13T14:20:37Z https://gatk.broadinstitute.org/hc/en-us/articles/9570410975899-IndelLength 2022-10-13T14:15:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570411057179-ValidateVariants 2022-10-13T14:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/9570411317659-CollectAllelicCounts 2022-10-13T14:20:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570411777179-FingerprintingSummaryMetrics 2022-10-13T14:15:42Z https://gatk.broadinstitute.org/hc/en-us/articles/9570412154139-ReblockGVCF 2022-10-13T14:19:37Z https://gatk.broadinstitute.org/hc/en-us/articles/9570412583451-FixMisencodedBaseQualityReads 2022-10-13T14:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570412672155-LeftAlignAndTrimVariants 2022-10-13T14:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570413009563-DuplicationMetrics 2022-10-13T14:13:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570413123355-RevertSamSpark-BETA 2022-10-13T14:19:42Z https://gatk.broadinstitute.org/hc/en-us/articles/9570414311579-GcContent 2022-10-13T14:14:04Z https://gatk.broadinstitute.org/hc/en-us/articles/9570414410267-CreateSequenceDictionary-Picard 2022-10-13T14:19:50Z https://gatk.broadinstitute.org/hc/en-us/articles/9570415011867-AllelePseudoDepth 2022-10-13T14:14:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570416018587-FlagStatSpark 2022-10-13T14:19:57Z https://gatk.broadinstitute.org/hc/en-us/articles/9570416554907-GetPileupSummaries 2022-10-13T14:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/9570417338779-GenotypeConcordanceDetailMetrics 2022-10-13T14:14:32Z https://gatk.broadinstitute.org/hc/en-us/articles/9570417526811-DownsampleSam-Picard 2022-10-13T14:20:05Z https://gatk.broadinstitute.org/hc/en-us/articles/9570417649307-ClippingRankSumTest 2022-10-13T14:14:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570417766811-VariantCallingDetailMetrics 2022-10-13T14:14:36Z https://gatk.broadinstitute.org/hc/en-us/articles/9570418730139-PossibleDeNovo 2022-10-13T14:14:46Z https://gatk.broadinstitute.org/hc/en-us/articles/9570419184923-BaseQualityRankSumTest 2022-10-13T14:14:50Z https://gatk.broadinstitute.org/hc/en-us/articles/9570419288219-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2022-10-13T14:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570419503259-ApplyVQSR 2022-10-13T14:20:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570421328411-ErrorSummaryMetrics 2022-10-13T14:14:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570421542811-ScatterIntervalsByNs-Picard 2022-10-13T14:20:18Z https://gatk.broadinstitute.org/hc/en-us/articles/9570422031771-BamIndexStats-Picard 2022-10-13T14:20:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570422171291-Mutect2 2022-10-13T14:20:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570422394907-TargetMetrics 2022-10-13T14:15:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570422529179-SVAnnotate 2023-10-10T03:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570423318427-CombineGVCFs 2022-10-13T14:20:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570424153115-AddOATag-Picard 2022-10-13T14:20:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570424337563-ReadPosition 2022-10-13T14:15:25Z https://gatk.broadinstitute.org/hc/en-us/articles/9570424536731-Coverage 2022-10-13T14:15:26Z https://gatk.broadinstitute.org/hc/en-us/articles/9570424849051-ApplyBQSRSpark-BETA 2022-10-13T14:20:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570425008923-CalculateGenotypePosteriors 2022-10-13T14:20:36Z https://gatk.broadinstitute.org/hc/en-us/articles/9570425188635-CollectMultipleMetrics-Picard 2022-10-13T14:20:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570426411803-PreprocessIntervals 2022-10-13T14:20:44Z https://gatk.broadinstitute.org/hc/en-us/articles/9570426618907-PrintDistantMates 2022-10-13T14:20:46Z https://gatk.broadinstitute.org/hc/en-us/articles/9570426714011-FlagStat 2022-10-13T14:20:47Z https://gatk.broadinstitute.org/hc/en-us/articles/9570426970395-IlluminaPhasingMetrics 2022-10-13T14:15:48Z https://gatk.broadinstitute.org/hc/en-us/articles/9570427046427-InbreedingCoeff 2022-10-13T14:15:49Z https://gatk.broadinstitute.org/hc/en-us/articles/9570427644443-FlowBasedTPAttributeValidReadFilter 2022-10-13T14:15:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570429984027-ReadNameReadFilter 2022-10-13T14:14:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570430059803-ExtractVariantAnnotations-BETA 2022-10-13T14:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570431743131-AddOrReplaceReadGroups-Picard 2022-10-13T14:15:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570434728091-ExtractSVEvidenceSpark-BETA 2022-10-13T14:20:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570435872027-CombineGenotypingArrayVcfs-Picard 2022-10-13T14:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/9570435962139-BaitDesigner-Picard 2022-10-13T14:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/9570436248603-ReadLengthEqualsCigarLengthReadFilter 2022-10-13T14:20:50Z https://gatk.broadinstitute.org/hc/en-us/articles/9570436376859-FixMateInformation-Picard 2022-10-13T14:15:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570436558107-PrintVariantsSpark 2022-10-13T14:20:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570437432987-MappingQualityZero 2022-10-13T14:14:57Z https://gatk.broadinstitute.org/hc/en-us/articles/9570438401691-CollectArraysVariantCallingMetrics-Picard 2022-10-13T14:20:22Z https://gatk.broadinstitute.org/hc/en-us/articles/9570439068187-PlotModeledSegments 2022-10-13T14:15:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570439565979-LocalAssembler-BETA 2022-10-13T14:20:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570440033179-LiftoverVcf-Picard 2022-10-13T14:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/9570440154779-ArraysVariantCallingSummaryMetrics 2022-10-13T14:15:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570440353179-ReadTagValueFilter 2022-10-13T14:15:24Z https://gatk.broadinstitute.org/hc/en-us/articles/9570440791835-ReadStrandFilter 2022-10-13T14:15:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570440864155-TargetedPcrMetrics 2022-10-13T14:15:28Z https://gatk.broadinstitute.org/hc/en-us/articles/9570442025115-CNNScoreVariants 2022-10-13T14:20:42Z https://gatk.broadinstitute.org/hc/en-us/articles/9570442136091-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2022-10-13T14:15:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570443636251-ValidateSamFile-Picard 2022-10-13T14:15:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570444169243-ReadGroupBlackListReadFilter 2022-10-13T14:15:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570444443931-SamToFastq-Picard 2022-10-13T14:20:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570445654427-TheoreticalSensitivityMetrics 2022-10-13T14:15:15Z https://gatk.broadinstitute.org/hc/en-us/articles/9570446093339-CollectGcBiasMetrics-Picard 2022-10-13T14:15:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570447592347-WellformedFlowBasedReadFilter 2023-01-16T22:16:50Z https://gatk.broadinstitute.org/hc/en-us/articles/9570448595099-MethylationTypeCaller-EXPERIMENTAL 2022-10-13T14:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/9570450093339-IndependentReplicateMetric 2022-10-13T14:15:56Z https://gatk.broadinstitute.org/hc/en-us/articles/9570450175643-FastqToSam-Picard 2022-10-13T14:20:56Z https://gatk.broadinstitute.org/hc/en-us/articles/9570450423707-WgsMetrics 2022-10-13T14:15:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570450655515-SortSam-Picard 2022-10-13T14:20:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570450770843-GcBiasDetailMetrics 2022-10-13T14:16:02Z https://gatk.broadinstitute.org/hc/en-us/articles/9570450882331-CollectIlluminaBasecallingMetrics-Picard 2022-10-13T14:16:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570450996507-FuncotatorDataSourceDownloader 2022-10-13T14:16:04Z https://gatk.broadinstitute.org/hc/en-us/articles/9570451123355-ConvertHeaderlessHadoopBamShardToBam-BETA 2022-10-13T14:16:05Z https://gatk.broadinstitute.org/hc/en-us/articles/9570455619995-PrintReadCounts-EXPERIMENTAL 2022-10-13T14:20:28Z https://gatk.broadinstitute.org/hc/en-us/articles/9570456420251-MateOnSameContigOrNoMappedMateReadFilter 2022-10-13T14:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/9570456913179-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2022-10-13T14:15:29Z https://gatk.broadinstitute.org/hc/en-us/articles/9570458186523-CpcgMetrics 2022-10-13T14:15:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570458549659-QualityScoreDistribution-Picard 2022-10-13T14:15:44Z https://gatk.broadinstitute.org/hc/en-us/articles/9570459377819-SortVcf-Picard 2022-10-13T14:20:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570459782043-BpmToNormalizationManifestCsv-Picard 2022-10-13T14:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570461322651-AnnotateIntervals 2022-10-13T14:21:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570461691675-AS-MappingQualityRankSumTest 2022-10-13T14:16:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570462129947-IntervalOverlapReadFilter 2022-10-13T14:16:18Z https://gatk.broadinstitute.org/hc/en-us/articles/9570465204763-PathSeqScoreSpark 2022-10-13T14:21:05Z https://gatk.broadinstitute.org/hc/en-us/articles/9570465652635-ReadPosRankSumTest 2022-10-13T14:16:15Z https://gatk.broadinstitute.org/hc/en-us/articles/9570465780635-BaseQuality 2022-10-13T14:16:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570466405659-GroundTruthReadsBuilder-EXPERIMENTAL 2022-10-13T14:21:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570466678811-VariantRecalibrator 2022-10-13T14:21:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570467568795-HmerIndelNuc 2022-10-13T14:16:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570468120987-JointGermlineCNVSegmentation-BETA 2022-10-13T14:21:22Z https://gatk.broadinstitute.org/hc/en-us/articles/9570470302747-BuildBamIndex-Picard 2022-10-13T14:21:36Z https://gatk.broadinstitute.org/hc/en-us/articles/9570470515355-NotSecondaryAlignmentReadFilter 2022-10-13T14:16:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570471670299-MergeSamFiles-Picard 2022-10-13T14:21:02Z https://gatk.broadinstitute.org/hc/en-us/articles/9570471757083-CollectRnaSeqMetrics-Picard 2022-10-13T14:16:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570474608795-StructuralVariationDiscoveryPipelineSpark-BETA 2022-10-13T14:21:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570474716699-EvaluateInfoFieldConcordance-BETA 2022-10-13T14:21:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570475259291-DepthOfCoverage-BETA 2022-10-13T14:21:23Z https://gatk.broadinstitute.org/hc/en-us/articles/9570476742043-AnalyzeSaturationMutagenesis-BETA 2022-10-13T14:21:33Z https://gatk.broadinstitute.org/hc/en-us/articles/9570477715483-IndelErrorMetric 2022-10-13T14:17:01Z https://gatk.broadinstitute.org/hc/en-us/articles/9570478284059-FingerprintingDetailMetrics 2022-10-13T14:17:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570479657371-GatherVcfsCloud-BETA 2022-10-13T14:16:08Z https://gatk.broadinstitute.org/hc/en-us/articles/9570480153627-SplitReads 2022-10-13T14:21:07Z https://gatk.broadinstitute.org/hc/en-us/articles/9570481026203-RampedHaplotypeCaller-EXPERIMENTAL 2022-10-13T14:21:11Z https://gatk.broadinstitute.org/hc/en-us/articles/9570482049947-CycleSkipStatus 2022-10-13T14:16:29Z https://gatk.broadinstitute.org/hc/en-us/articles/9570482155419-UnmarkDuplicates 2022-10-13T14:21:19Z https://gatk.broadinstitute.org/hc/en-us/articles/9570483314331-BaseErrorMetric 2022-10-13T14:16:40Z https://gatk.broadinstitute.org/hc/en-us/articles/9570484449435-FindBadGenomicKmersSpark-BETA 2023-03-10T21:56:59Z https://gatk.broadinstitute.org/hc/en-us/articles/9570484541979-AddCommentsToBam-Picard 2022-10-13T14:21:33Z https://gatk.broadinstitute.org/hc/en-us/articles/9570484693019-AS-QualByDepth 2022-10-13T14:21:34Z https://gatk.broadinstitute.org/hc/en-us/articles/9570484756507-AS-BaseQualityRankSumTest 2022-10-13T14:16:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570484838043-Concordance 2022-10-13T14:21:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570485677339-ReferenceBases 2022-10-13T14:17:03Z https://gatk.broadinstitute.org/hc/en-us/articles/9570485876379-MetricsReadFilter 2022-10-13T14:17:05Z https://gatk.broadinstitute.org/hc/en-us/articles/9570487170587-ReadAnonymizer-EXPERIMENTAL 2022-10-13T14:21:49Z https://gatk.broadinstitute.org/hc/en-us/articles/9570487315995-MappingQualityAvailableReadFilter 2022-10-13T14:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/9570487998491-SplitNCigarReads 2022-10-13T14:21:21Z https://gatk.broadinstitute.org/hc/en-us/articles/9570488084763-NonZeroFragmentLengthReadFilter 2022-10-13T14:16:35Z https://gatk.broadinstitute.org/hc/en-us/articles/9570488849691-CigarContainsNoNOperator 2022-10-13T14:16:42Z https://gatk.broadinstitute.org/hc/en-us/articles/9570489068699-SplitSamByLibrary-Picard 2022-10-13T14:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/9570489180699-CrosscheckFingerprints-Picard 2022-10-13T14:21:30Z https://gatk.broadinstitute.org/hc/en-us/articles/9570489472411-GenotypeGVCFs 2022-10-26T03:01:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570490238619-FragmentLengthReadFilter 2022-10-13T14:16:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570491346715-FastaReferenceMaker 2022-10-13T14:21:43Z https://gatk.broadinstitute.org/hc/en-us/articles/9570491804571-ConvertSequencingArtifactToOxoG-Picard 2022-10-13T14:17:11Z https://gatk.broadinstitute.org/hc/en-us/articles/9570493214363-CountBasesSpark 2022-10-13T14:21:52Z https://gatk.broadinstitute.org/hc/en-us/articles/9570493644059-FilterVariantTranches 2022-10-13T14:21:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570496016667-RevertSam-Picard 2022-10-13T14:21:06Z https://gatk.broadinstitute.org/hc/en-us/articles/9570496091035-PassesVendorQualityCheckReadFilter 2022-10-13T14:16:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570496580635-SeqIsStoredReadFilter 2022-10-13T14:16:17Z https://gatk.broadinstitute.org/hc/en-us/articles/9570497528987-PathSeqFilterSpark 2023-02-12T12:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570497651739-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2022-10-13T14:21:15Z https://gatk.broadinstitute.org/hc/en-us/articles/9570497734683-PlotDenoisedCopyRatios 2022-10-13T14:16:26Z https://gatk.broadinstitute.org/hc/en-us/articles/9570497987995-FastaAlternateReferenceMaker 2022-10-13T14:21:17Z https://gatk.broadinstitute.org/hc/en-us/articles/9570499300891-ProperlyPairedReadFilter 2022-10-13T14:16:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570499963547-CNNVariantTrain-EXPERIMENTAL 2022-10-13T14:21:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570500202395-TandemRepeat 2022-10-13T14:16:49Z https://gatk.broadinstitute.org/hc/en-us/articles/9570501013659-CollectRrbsMetrics-Picard 2022-10-13T14:16:58Z https://gatk.broadinstitute.org/hc/en-us/articles/9570501280795-WgsMetricsWithNonZeroCoverage 2022-10-13T14:17:01Z https://gatk.broadinstitute.org/hc/en-us/articles/9570501436827-ShiftFasta-BETA 2022-10-13T14:21:39Z https://gatk.broadinstitute.org/hc/en-us/articles/9570501730203-ValidAlignmentEndReadFilter 2022-10-13T14:21:41Z https://gatk.broadinstitute.org/hc/en-us/articles/9570502238619-AlleleFraction 2022-10-13T14:17:10Z https://gatk.broadinstitute.org/hc/en-us/articles/9570502711707-CountNs 2022-10-13T14:17:14Z https://gatk.broadinstitute.org/hc/en-us/articles/9570503206043-CollectOxoGMetrics-Picard 2022-10-13T14:17:18Z https://gatk.broadinstitute.org/hc/en-us/articles/9570505180315-DepthPerSampleHC 2022-10-13T14:17:09Z https://gatk.broadinstitute.org/hc/en-us/articles/9570505688475-AssemblyComplexity 2022-10-13T14:17:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570507142683-ASEReadCounter 2022-10-13T14:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570512602523-NonZeroReferenceLengthAlignmentReadFilter 2023-01-13T08:40:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570513026459-CollectBaseDistributionByCycleSpark-BETA 2022-10-13T14:21:13Z https://gatk.broadinstitute.org/hc/en-us/articles/9570513631387-SplitIntervals 2022-10-13T14:21:17Z https://gatk.broadinstitute.org/hc/en-us/articles/9570514937115-PileupSpark-BETA 2022-10-13T14:21:24Z https://gatk.broadinstitute.org/hc/en-us/articles/9570515301787-SplitVcfs-Picard 2022-10-13T14:21:27Z https://gatk.broadinstitute.org/hc/en-us/articles/9570515405211-FilterFuncotations-EXPERIMENTAL 2022-10-13T14:21:29Z https://gatk.broadinstitute.org/hc/en-us/articles/9570517002523-FindMendelianViolations-Picard 2022-10-13T14:21:38Z https://gatk.broadinstitute.org/hc/en-us/articles/9570517384731-IndexFeatureFile 2022-10-13T14:17:04Z https://gatk.broadinstitute.org/hc/en-us/articles/9570517922459-QualityScoreDistributionSpark-BETA 2022-10-13T14:21:43Z https://gatk.broadinstitute.org/hc/en-us/articles/9570518369179-OrientationBiasReadCounts 2022-10-13T14:17:12Z https://gatk.broadinstitute.org/hc/en-us/articles/9570519248411-CreateReadCountPanelOfNormals 2022-10-13T14:17:19Z https://gatk.broadinstitute.org/hc/en-us/articles/9570520368411-HmerMotifs 2022-10-13T14:17:30Z https://gatk.broadinstitute.org/hc/en-us/articles/9570521306267-CollectDuplicateMetrics-Picard 2022-10-13T14:17:20Z https://gatk.broadinstitute.org/hc/en-us/articles/9570521694747-PrintReadsSpark 2022-10-13T14:21:53Z https://gatk.broadinstitute.org/hc/en-us/articles/9570522238491-CheckPileup 2022-10-13T14:21:56Z https://gatk.broadinstitute.org/hc/en-us/articles/9570522386203-GtcToVcf-Picard 2022-10-13T14:17:29Z https://gatk.broadinstitute.org/hc/en-us/articles/9570522637339-CheckTerminatorBlock-Picard 2022-10-13T14:17:31Z https://gatk.broadinstitute.org/hc/en-us/articles/9570529725979-RenameSampleInVcf-Picard 2022-10-13T14:21:47Z https://gatk.broadinstitute.org/hc/en-us/articles/9570530581659-CountReadsSpark 2022-10-13T14:21:51Z https://gatk.broadinstitute.org/hc/en-us/articles/9570531065115-CalibrateDragstrModel 2022-10-13T14:21:54Z https://gatk.broadinstitute.org/hc/en-us/articles/9570531313563-CreateSomaticPanelOfNormals-BETA 2022-10-13T14:21:55Z https://gatk.broadinstitute.org/hc/en-us/articles/9570531983643-CleanSam-Picard 2022-10-13T14:17:33Z https://gatk.broadinstitute.org/hc/en-us/articles/9570538261659-ReadLengthReadFilter 2022-10-13T14:17:32Z https://gatk.broadinstitute.org/hc/en-us/articles/10064202674971-Introducing-NVIDIA-s-NVScoreVariants-a-new-deep-learning-tool-for-filtering-variants 2025-09-16T07:17:16Z https://gatk.broadinstitute.org/hc/en-us/articles/10082764643867--GATK-4-3-release 2024-07-01T17:07:12Z https://gatk.broadinstitute.org/hc/en-us/articles/10757052577947-DRAGEN-GATK-Webinar-December-3-2021 2024-07-08T20:08:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626034203-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2023-03-20T19:27:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626103451-ChromosomeCounts 2023-03-20T19:22:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626170267-LibraryReadFilter 2023-03-20T19:22:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626233627-DumpTabixIndex 2023-03-20T19:22:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626294939-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2023-03-20T19:22:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626369691-NonChimericOriginalAlignmentReadFilter 2023-03-20T19:22:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626469787-MeanQualityByCycle-Picard 2023-03-20T19:27:45Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626514459-CollectHiSeqXPfFailMetrics-Picard 2023-03-20T19:22:58Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626568987-GenotypeConcordance-Picard 2023-03-20T19:27:45Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626610459-Pileup 2023-03-20T19:27:46Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626740379-BwaMemIndexImageCreator 2023-03-20T19:27:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832626880795-NotProperlyPairedReadFilter 2023-03-20T19:23:01Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627047835-BarcodeMetric 2023-03-20T19:23:03Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627111067-WellformedReadFilter 2023-03-20T19:27:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627271963-AnalyzeCovariates 2023-03-20T19:27:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627338523-RMSMappingQuality 2023-03-20T19:23:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627472539-Funcotator 2023-03-20T19:27:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627552795-CollectQualityYieldMetrics-Picard 2023-03-20T19:23:08Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627644443-PathSeqPipelineSpark 2023-03-20T19:27:51Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627727131-CalcMetadataSpark-BETA 2023-03-20T19:27:52Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627804059-SecondOfPairReadFilter 2023-03-20T19:23:10Z https://gatk.broadinstitute.org/hc/en-us/articles/13832627925531-AS-StrandOddsRatio 2023-03-20T19:23:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832628282907-RnaSeqMetrics 2023-03-20T19:23:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832628346779-CountReads 2023-03-20T19:27:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832628512411-AccumulateQualityYieldMetrics-Picard 2023-03-20T19:23:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832628584219-IlluminaBasecallingMetrics 2023-03-20T19:23:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832628653979-GnarlyGenotyper-BETA 2023-03-20T19:27:57Z https://gatk.broadinstitute.org/hc/en-us/articles/13832628867099-PrintReadsHeader 2023-03-20T19:27:58Z https://gatk.broadinstitute.org/hc/en-us/articles/13832629156251-CountVariants 2023-03-20T19:28:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832629222811-AllowAllReadsReadFilter 2023-05-08T11:16:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832629347099-NotDuplicateReadFilter 2023-03-20T19:23:26Z https://gatk.broadinstitute.org/hc/en-us/articles/13832629482779-BamToBfq-Picard 2023-03-20T19:23:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832629642267-ArraysControlCodesSummaryMetrics 2023-03-20T19:23:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832629767579-FilterSamReads-Picard 2023-03-20T19:28:03Z https://gatk.broadinstitute.org/hc/en-us/articles/13832629830683-MergePedIntoVcf-Picard 2023-03-20T19:23:32Z https://gatk.broadinstitute.org/hc/en-us/articles/13832630023835-CollectMultipleMetricsSpark-BETA 2023-03-20T19:28:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832651527835-OverclippedReadFilter 2023-03-20T19:23:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832651666459-VerifyIDIntensityContaminationMetrics 2023-03-20T19:23:01Z https://gatk.broadinstitute.org/hc/en-us/articles/13832651831579-ExcessiveEndClippedReadFilter 2023-03-20T19:23:02Z https://gatk.broadinstitute.org/hc/en-us/articles/13832652059931-SampleReadFilter 2023-03-20T19:23:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832652297627-FirstOfPairReadFilter 2023-03-20T19:23:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832652772763-AlignmentAgreesWithHeaderReadFilter 2023-03-20T19:23:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832652896539-FilterVcf-Picard 2023-03-20T19:23:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832652976155-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2023-03-20T19:27:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653055387-VariantEval-BETA 2023-03-20T19:23:14Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653132187-GcBiasSummaryMetrics 2023-03-20T19:23:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653319451-FixVcfHeader-Picard 2023-03-20T19:27:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653377179-CollectHsMetrics-Picard 2023-03-20T19:27:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653631259-JumpingLibraryMetrics 2023-03-20T19:23:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653713819-EstimateLibraryComplexity-Picard 2023-03-20T19:23:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653838747-ViewSam-Picard 2023-03-20T19:27:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653900955-AnnotateVcfWithExpectedAlleleFraction 2023-03-20T19:27:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832653972379-ErrorMetric 2023-03-20T19:23:23Z https://gatk.broadinstitute.org/hc/en-us/articles/13832654193307-LiftOverIntervalList-Picard 2023-03-20T19:23:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832654286235-OverlappingErrorMetric 2023-03-20T19:23:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832654377243-VariantCallingSummaryMetrics 2023-03-20T19:23:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832654422811-PreAdapterSummaryMetrics 2023-03-20T19:23:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator 2024-03-08T00:26:45Z https://gatk.broadinstitute.org/hc/en-us/articles/13832654766875-PrimaryLineReadFilter 2023-03-20T19:23:32Z https://gatk.broadinstitute.org/hc/en-us/articles/13832654835099-BafRegressMetrics 2023-03-20T19:23:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832655089563-StrandOddsRatio 2023-03-20T19:23:35Z https://gatk.broadinstitute.org/hc/en-us/articles/13832655155099--Tool-Documentation-Index 2023-03-20T19:28:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832680428571-CompareReferences-EXPERIMENTAL 2023-03-20T19:28:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832680477595-CountBases 2023-03-20T19:28:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832680680091-MendelianViolationMetrics 2023-03-20T19:23:37Z https://gatk.broadinstitute.org/hc/en-us/articles/13832680742811-CheckFingerprint-Picard 2023-03-20T19:23:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832680794267-HasReadGroupReadFilter 2023-03-20T19:23:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832680852635-DetermineGermlineContigPloidy 2023-10-12T03:47:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832680917787-FindBreakpointEvidenceSpark-BETA 2023-03-20T19:28:08Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681060123-MappingQuality 2023-03-20T19:23:41Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681160475-QualByDepth 2023-03-20T19:23:42Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681309083-VariantsToTable 2023-03-20T19:28:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681398939-HaplotypeBasedVariantRecaller-EXPERIMENTAL 2023-03-20T19:28:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681504539-AS-RMSMappingQuality 2023-03-20T19:23:46Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681555227-PFFailSummaryMetric 2023-03-20T19:23:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681869723-SamFormatConverter-Picard 2023-03-20T19:23:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832681986587-FisherStrand 2023-03-20T19:23:52Z https://gatk.broadinstitute.org/hc/en-us/articles/13832682084251-ClusterCrosscheckMetrics-Picard 2023-03-20T19:23:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832682197019-CollectSamErrorMetrics-Picard 2023-03-20T19:23:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832682540699-MarkDuplicatesSpark 2023-09-14T13:28:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832682586651-DepthPerAlleleBySample 2023-03-20T19:23:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832682871835-GcBiasMetrics 2023-03-20T19:24:01Z https://gatk.broadinstitute.org/hc/en-us/articles/13832683056539-FuncotateSegments-BETA 2023-03-20T19:28:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832683213851-BaitBiasSummaryMetrics 2023-03-20T19:24:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832683285787-CalculateFingerprintMetrics-Picard 2023-03-20T19:24:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832683345947-PathSeqBuildReferenceTaxonomy 2023-03-20T19:24:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832683660955-CollectAlignmentSummaryMetrics-Picard 2023-03-20T19:24:09Z https://gatk.broadinstitute.org/hc/en-us/articles/13832683803419-CollectSequencingArtifactMetrics-Picard 2023-03-20T19:24:10Z https://gatk.broadinstitute.org/hc/en-us/articles/13832683937435-GatherVcfs-Picard 2023-03-20T19:24:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684003739-MappedReadFilter 2023-03-20T19:24:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684066843-ExtractSequences-Picard 2023-03-20T19:28:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684165275-GatherBQSRReports 2023-03-20T19:24:14Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684230939-CalculateContamination 2023-03-20T19:28:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684466587-PathSeqBuildKmers 2023-03-20T19:28:30Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684599067-IntervalListTools-Picard 2023-03-20T19:28:31Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684666139-CollectInsertSizeMetrics-Picard 2023-03-20T19:24:19Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684727451-StrandBiasBySample 2023-03-20T19:24:19Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684824475-FragmentDepthPerAlleleBySample 2023-03-20T19:24:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684939419-CollectReadCounts 2023-03-20T19:28:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832684987547-InsertSizeMetrics 2023-03-20T19:24:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685033243-SortSamSpark-BETA 2023-03-20T19:28:34Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685087003-LeftAlignIndels 2023-03-20T19:28:34Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685193371-MappingQualityRankSumTest 2023-03-20T19:24:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685277467-MappingQualityNotZeroReadFilter 2023-03-20T19:24:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685403803-HaplotypeCallerSpark-BETA 2023-03-20T19:28:36Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685705243-MateDifferentStrandReadFilter 2023-03-20T19:28:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685767323-NonNFastaSize-Picard 2023-03-20T19:28:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832685893403-FingerprintMetrics 2023-03-20T19:24:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686056475-BaitBiasDetailMetrics 2023-03-20T19:24:35Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686099611-CalculateMixingFractions 2023-03-20T19:28:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686245787-AccumulateVariantCallingMetrics-Picard 2023-03-20T19:24:37Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686320923-IlluminaBasecallsToSam-Picard 2023-03-20T19:24:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686400539-SVCluster-BETA 2023-03-20T19:28:42Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686452635-ScoreVariantAnnotations-BETA 2023-03-20T19:28:42Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686523419-ReadGroupReadFilter 2023-03-20T19:24:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686645787-GenomicsDBImport 2025-05-08T18:30:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686749339-PlatformUnitReadFilter 2023-03-20T19:24:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686808731-CreateBafRegressMetricsFile-Picard 2023-03-20T19:24:44Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686917275-CreateHadoopBamSplittingIndex-BETA 2023-03-20T19:24:45Z https://gatk.broadinstitute.org/hc/en-us/articles/13832686984219-PrintReads 2023-03-20T19:28:46Z https://gatk.broadinstitute.org/hc/en-us/articles/13832687045019-GenotypeConcordanceSummaryMetrics 2023-03-20T19:24:46Z https://gatk.broadinstitute.org/hc/en-us/articles/13832687103131-HmerQualitySymetricReadFilter 2023-03-20T19:24:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832687162139-BwaAndMarkDuplicatesPipelineSpark-BETA 2023-03-20T19:28:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832687299739-HaplotypeCaller 2023-03-20T19:28:48Z https://gatk.broadinstitute.org/hc/en-us/articles/13832687360411-AlignmentSummaryMetrics 2023-03-20T19:24:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832687775643-CountBasesInReference 2023-03-20T19:28:51Z https://gatk.broadinstitute.org/hc/en-us/articles/13832688099483-PathSeqBwaSpark 2023-03-20T19:28:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832688210587-SampleList 2023-03-20T19:25:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832688342555-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2023-03-20T19:28:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832688540699-CheckIlluminaDirectory-Picard 2023-03-20T19:28:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832688611995-CollectTargetedPcrMetrics-Picard 2023-03-20T19:28:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832688660507-CollectBaseDistributionByCycle-Picard 2023-03-20T19:25:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832688703387-RrbsSummaryMetrics 2023-03-20T19:25:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689110683-UniqueAltReadCount 2023-03-20T19:23:41Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689352731-FlowFeatureMapper-EXPERIMENTAL 2023-03-20T19:28:10Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689399707-FlowBasedTPAttributeSymetricReadFilter 2023-03-20T19:23:44Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689613595-NormalizeFasta-Picard 2023-03-20T19:28:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689780123-CNNVariantWriteTensors-EXPERIMENTAL 2023-03-20T19:28:13Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689851035-CountVariantsSpark 2023-03-20T19:23:48Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689927835-UpdateVCFSequenceDictionary 2023-03-20T19:28:13Z https://gatk.broadinstitute.org/hc/en-us/articles/13832689986843-IlluminaBasecallsToFastq-Picard 2023-03-20T19:23:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690093851-PostProcessReadsForRSEM-BETA 2023-03-20T19:28:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690201371-GeneExpressionEvaluation-BETA 2023-03-20T19:28:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690289947-ClipReads 2023-03-20T19:28:16Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690402075-ReadGroupHasFlowOrderReadFilter 2023-03-20T19:23:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690451355-SoftClippedReadFilter 2023-03-20T19:23:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690497179-GetSampleName 2023-03-20T19:28:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690555035-CollectSVEvidence-BETA 2023-03-20T19:28:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690613659-SiteDepthtoBAF-EXPERIMENTAL 2023-03-20T19:28:19Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690815899-CalculateReadGroupChecksum-Picard 2023-03-20T19:28:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690881691-HaplotypeFilteringAnnotation 2023-03-20T19:24:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832690946075-SetNmMdAndUqTags-Picard 2023-03-20T19:28:21Z https://gatk.broadinstitute.org/hc/en-us/articles/13832691120667-CompareMetrics-Picard 2023-03-20T19:28:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832691289499-GatherBamFiles-Picard 2023-03-20T19:24:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832691588251-AS-FisherStrand 2023-03-20T19:24:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832691655579-CompareBaseQualities 2023-03-20T19:24:07Z https://gatk.broadinstitute.org/hc/en-us/articles/13832691713947-BwaSpark-BETA 2023-03-20T19:28:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832691782939-SamComparisonMetric 2023-03-20T19:24:08Z https://gatk.broadinstitute.org/hc/en-us/articles/13832691909403-AnnotateVcfWithBamDepth 2023-03-20T19:28:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832692021275-GenotypeConcordanceContingencyMetrics 2023-03-20T19:24:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832692277275-MarkDuplicatesWithMateCigar-Picard 2023-03-20T19:28:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832692459163-ApplyBQSR 2023-03-20T19:28:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832692538779-CpxVariantReInterpreterSpark-BETA 2023-03-20T19:28:30Z https://gatk.broadinstitute.org/hc/en-us/articles/13832692695835-MakeSitesOnlyVcf-Picard 2023-03-20T19:28:31Z https://gatk.broadinstitute.org/hc/en-us/articles/13832692984347-LearnReadOrientationModel 2023-03-20T19:24:21Z https://gatk.broadinstitute.org/hc/en-us/articles/13832693277595-FilterIntervals 2023-10-17T11:42:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832693486747-GetNormalArtifactData 2023-03-20T19:28:35Z https://gatk.broadinstitute.org/hc/en-us/articles/13832693617691-CollectJumpingLibraryMetrics-Picard 2023-03-20T19:24:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832693663899-SplitSamByNumberOfReads-Picard 2023-03-20T19:28:37Z https://gatk.broadinstitute.org/hc/en-us/articles/13832693720603-HsMetrics 2023-03-20T19:24:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832693780635-ComposeSTRTableFile 2023-03-20T19:28:37Z https://gatk.broadinstitute.org/hc/en-us/articles/13832694001563-FilterMutectCalls 2023-03-20T19:28:39Z https://gatk.broadinstitute.org/hc/en-us/articles/13832694104987-BaseRecalibratorSpark-BETA 2023-03-20T19:28:39Z https://gatk.broadinstitute.org/hc/en-us/articles/13832694334235-SelectVariants 2023-03-20T19:28:41Z https://gatk.broadinstitute.org/hc/en-us/articles/13832694739867-MappingQualityReadFilter 2023-03-20T19:28:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832694875547-CollectQualityYieldMetricsSpark-BETA 2023-03-20T19:28:44Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695051163-RawGtCount 2023-03-20T19:24:44Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695383451-MateDistantReadFilter 2023-03-20T19:28:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695570331-ValidAlignmentStartReadFilter 2023-03-20T19:28:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695649691-ReadsPipelineSpark-BETA 2023-03-20T19:28:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695699355-ReplaceSamHeader-Picard 2023-03-20T19:28:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695751195-CountFalsePositives-BETA 2023-03-20T19:28:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695802779-MateUnmappedAndUnmappedReadFilter 2023-03-20T19:24:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695842587-CollectIlluminaLaneMetrics-Picard 2023-03-20T19:24:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695938587-ClusteredCrosscheckMetric 2023-03-20T19:24:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832695988635-JexlExpressionReadTagValueFilter 2023-03-20T19:24:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832696066331-VcfToIntervalList-Picard 2023-03-20T19:28:52Z https://gatk.broadinstitute.org/hc/en-us/articles/13832696108571-SetNmAndUqTags-Picard 2023-03-20T19:28:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832696268827-MarkIlluminaAdapters-Picard 2023-03-20T19:28:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832696371739-MatchingBasesAndQualsReadFilter 2023-03-20T19:25:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832696549787-MeanQualityByCycleSpark-BETA 2023-03-20T19:28:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832696621467-FragmentLength 2023-03-20T19:25:02Z https://gatk.broadinstitute.org/hc/en-us/articles/13832696945307-ReblockGVCF 2023-03-20T19:28:57Z https://gatk.broadinstitute.org/hc/en-us/articles/13832697082907-TrainVariantAnnotationsModel-BETA 2023-03-20T19:28:58Z https://gatk.broadinstitute.org/hc/en-us/articles/13832697141147-MergeBamAlignment-Picard 2023-03-20T19:25:08Z https://gatk.broadinstitute.org/hc/en-us/articles/13832705633307-RrbsCpgDetailMetrics 2023-03-20T19:25:07Z https://gatk.broadinstitute.org/hc/en-us/articles/13832705838235-LeftAlignAndTrimVariants 2023-03-20T19:28:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832706281627-AmbiguousBaseReadFilter 2023-03-20T19:25:14Z https://gatk.broadinstitute.org/hc/en-us/articles/13832706340763-BedToIntervalList-Picard 2023-03-20T19:29:02Z https://gatk.broadinstitute.org/hc/en-us/articles/13832706462491-CompareDuplicatesSpark-BETA 2023-03-20T19:29:03Z https://gatk.broadinstitute.org/hc/en-us/articles/13832706644379-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2023-03-20T19:29:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832706923035-VcfToAdpc-Picard 2023-03-20T19:25:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832706962971-GoodCigarReadFilter 2023-03-20T19:25:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707119771-AllelePseudoDepth 2023-03-20T19:25:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707217179-CheckReferenceCompatibility-EXPERIMENTAL 2023-03-20T19:29:07Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707345179-ReorderSam-Picard 2023-03-20T19:25:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707402267-RawWgsMetrics 2023-03-20T19:25:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707574555-BaseDistributionByCycleMetrics 2023-03-20T19:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707692571-FlagStatSpark 2023-03-20T19:29:10Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707791771-FilterAlignmentArtifacts-EXPERIMENTAL 2023-03-20T19:29:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707851035-CollectWgsMetrics-Picard 2023-03-20T19:25:32Z https://gatk.broadinstitute.org/hc/en-us/articles/13832707903643-UmiMetrics 2023-03-20T19:25:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708003995-AS-ReadPosRankSumTest 2023-03-20T19:25:34Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708323611-LikelihoodRankSumTest 2023-03-20T19:25:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708374939-BaseRecalibrator 2026-03-16T17:47:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708500763-GenotypeConcordanceDetailMetrics 2023-03-20T19:25:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708541851-GatherTranches-BETA 2023-03-20T19:25:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708637467-DownsampleSam-Picard 2023-03-20T19:29:16Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708735771-ClippingRankSumTest 2023-03-20T19:25:42Z https://gatk.broadinstitute.org/hc/en-us/articles/13832708964379-BQSRPipelineSpark-BETA 2023-03-20T19:29:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709037595-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2023-03-20T19:29:19Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709077787-ArraysVariantCallingDetailMetrics 2023-03-20T19:25:45Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709443995-BaseQualityRankSumTest 2023-03-20T19:25:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709627675-ApplyVQSR 2023-03-20T19:29:23Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709695259-GermlineCNVCaller 2023-03-20T19:25:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709748763-UpdateVcfSequenceDictionary-Picard 2023-03-20T19:25:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709873563-ExtractVariantAnnotations-BETA 2023-03-20T19:29:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832709960603-ErrorSummaryMetrics 2023-03-20T19:25:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710157851-PlatformReadFilter 2023-03-20T19:25:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710211867-QualityYieldMetrics 2023-03-20T19:25:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710257307-IlluminaLaneMetrics 2023-03-20T19:26:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710384155-Mutect2 2023-03-20T19:29:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710458267-CollectArraysVariantCallingMetrics-Picard 2023-03-20T19:29:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710678043-VariantType 2023-03-20T19:26:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710921371-TheoreticalSensitivityMetrics 2023-03-20T19:26:07Z https://gatk.broadinstitute.org/hc/en-us/articles/13832710975771-CombineGVCFs 2023-12-21T02:18:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711033115-LocalAssembler-BETA 2023-03-20T19:29:32Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711132315-CollectGcBiasMetrics-Picard 2023-03-20T19:26:10Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711413147-ReadPosition 2023-03-20T19:26:13Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711460251-MateOnSameContigOrNoMappedMateReadFilter 2023-03-20T19:29:36Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711528603-Coverage 2023-03-20T19:26:14Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711594267-ReadStrandFilter 2023-03-20T19:26:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711654811-TargetedPcrMetrics 2023-03-20T19:26:16Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711710107-ApplyBQSRSpark-BETA 2023-03-20T19:29:37Z https://gatk.broadinstitute.org/hc/en-us/articles/13832711858075-CalculateGenotypePosteriors 2023-03-20T19:29:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712028827-WellformedFlowBasedReadFilter 2023-03-20T19:29:39Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712128539-ValidateVariants 2023-03-20T19:29:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712179611-ExtractSVEvidenceSpark-BETA 2023-03-20T19:29:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712299547-CNNScoreVariants 2023-03-20T19:29:41Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712343835-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2023-03-20T19:26:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712391963-CpcgMetrics 2023-03-20T19:26:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712515611-FingerprintingSummaryMetrics 2023-03-20T19:26:26Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712713627-PrintDistantMates 2023-03-20T19:29:44Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712759579-FlagStat 2023-03-20T19:29:45Z https://gatk.broadinstitute.org/hc/en-us/articles/13832712803227-CombineGenotypingArrayVcfs-Picard 2023-03-20T19:29:45Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713008283-ReadLengthEqualsCigarLengthReadFilter 2023-03-20T19:29:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713065755-FixMateInformation-Picard 2023-03-20T19:26:32Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713101339-SortVcf-Picard 2023-03-20T19:29:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713174427-ValidateSamFile-Picard 2023-03-20T19:26:34Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713280155-BpmToNormalizationManifestCsv-Picard 2023-03-20T19:29:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713322395-IndependentReplicateMetric 2023-03-20T19:26:36Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713473563-WgsMetrics 2023-03-20T19:26:38Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713514139-SamToFastq-Picard 2023-03-20T19:29:51Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713565083-SortSam-Picard 2023-03-20T19:29:51Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713588763-GcBiasDetailMetrics 2023-03-20T19:26:39Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713641883-CollectIlluminaBasecallingMetrics-Picard 2023-03-20T19:26:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832713913499-AnnotateIntervals 2025-10-23T14:03:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832747547419-FixMisencodedBaseQualityReads 2023-03-20T19:28:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832747657883-ModelSegments 2023-03-20T19:28:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832747727003-FeaturizedReadSets 2023-03-20T19:25:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832747812763-DuplicationMetrics 2023-03-20T19:25:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832747863579-RevertSamSpark-BETA 2023-03-20T19:29:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832747915291-ExtractIlluminaBarcodes-Picard 2023-03-20T19:25:13Z https://gatk.broadinstitute.org/hc/en-us/articles/13832747964187-PFFailDetailedMetric 2023-03-20T19:25:14Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748157723-RemoveNearbyIndels 2023-03-20T19:29:02Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748311067-CollectRawWgsMetrics-Picard 2023-03-20T19:29:03Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748360091-HmerIndelLength 2023-03-20T19:25:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748460315-OriginalAlignment 2023-03-20T19:25:19Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748517275-MarkDuplicates-Picard 2023-03-20T19:25:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748569115-GcContent 2023-03-20T19:25:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748622491-CreateSequenceDictionary-Picard 2023-03-20T19:29:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748825499-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2023-03-20T19:25:23Z https://gatk.broadinstitute.org/hc/en-us/articles/13832748945947-PositionBasedDownsampleSam-Picard 2023-03-20T19:25:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749097627-PreAdapterDetailMetrics 2023-03-20T19:25:26Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749304347-PostprocessGermlineCNVCalls 2023-03-20T19:29:09Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749354267-NotSupplementaryAlignmentReadFilter 2023-03-20T19:25:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749454107-GenotypeSummaries 2023-03-20T19:25:30Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749726747-PairedReadFilter 2023-03-20T19:25:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749845403-GetPileupSummaries 2023-03-20T19:29:13Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749912091-FifoBuffer-Picard 2023-03-20T19:25:36Z https://gatk.broadinstitute.org/hc/en-us/articles/13832749998747-ExcessHet 2023-03-20T19:25:36Z https://gatk.broadinstitute.org/hc/en-us/articles/13832750065947-VariantFiltration 2023-03-20T19:29:14Z https://gatk.broadinstitute.org/hc/en-us/articles/13832750240155-RevertBaseQualityScores 2023-03-20T19:29:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832750623131-VariantCallingDetailMetrics 2023-03-20T19:25:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832750672923-CompareSAMs-Picard 2023-03-20T19:29:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832750881563-TransferReadTags-EXPERIMENTAL 2023-03-20T19:29:19Z https://gatk.broadinstitute.org/hc/en-us/articles/13832750934299-IndelClassify 2023-03-20T19:25:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832750995739-PossibleDeNovo 2023-03-20T19:25:48Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751062811-CollectInsertSizeMetricsSpark-BETA 2023-03-20T19:29:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751133851-DenoiseReadCounts 2023-03-20T19:25:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751258267-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2023-03-20T19:29:21Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751319835-IntervalListToBed-Picard 2023-03-20T19:25:51Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751571611-ReadNameReadFilter 2023-03-20T19:25:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751683995-MappingQualityZero 2023-03-20T19:25:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751795227-CallCopyRatioSegments 2023-03-20T19:25:57Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751853467-ScatterIntervalsByNs-Picard 2023-03-20T19:29:26Z https://gatk.broadinstitute.org/hc/en-us/articles/13832751907995-AS-InbreedingCoeff 2023-03-20T19:25:58Z https://gatk.broadinstitute.org/hc/en-us/articles/13832752212763-BamIndexStats-Picard 2023-03-20T19:29:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832752461467-TargetMetrics 2023-03-20T19:26:03Z https://gatk.broadinstitute.org/hc/en-us/articles/13832752531355-SVAnnotate 2023-03-20T19:29:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832752657819-VcfFormatConverter-Picard 2023-03-20T19:29:30Z https://gatk.broadinstitute.org/hc/en-us/articles/13832752709403-AddOrReplaceReadGroups-Picard 2023-03-20T19:26:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832752761243-PlotModeledSegments 2023-03-20T19:26:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832752810651-CollectVariantCallingMetrics-Picard 2023-03-20T19:26:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753006747-PrintReadCounts-EXPERIMENTAL 2023-03-20T19:29:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753098907-LiftoverVcf-Picard 2023-03-20T19:29:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753161627-ArraysVariantCallingSummaryMetrics 2023-03-20T19:26:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753232155-AddOATag-Picard 2023-03-20T19:29:34Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753284379-ReadTagValueFilter 2023-03-20T19:26:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753704731-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2023-03-20T19:26:17Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753837467-MergeVcfs-Picard 2023-08-29T15:53:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832753924763-CollectMultipleMetrics-Picard 2023-03-20T19:29:39Z https://gatk.broadinstitute.org/hc/en-us/articles/13832754036123-IndelLength 2023-03-20T19:26:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832754187035-CollectAllelicCounts 2025-09-24T15:40:30Z https://gatk.broadinstitute.org/hc/en-us/articles/13832754457499-MethylationTypeCaller-EXPERIMENTAL 2023-03-20T19:29:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832754597915-PreprocessIntervals 2023-03-20T19:29:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832754678171-QualityScoreDistribution-Picard 2023-03-20T19:26:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832754900891-BaitDesigner-Picard 2023-03-20T19:29:46Z https://gatk.broadinstitute.org/hc/en-us/articles/13832754965019-IlluminaPhasingMetrics 2023-03-20T19:26:30Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755011099-InbreedingCoeff 2023-03-20T19:26:31Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755184155-PrintVariantsSpark 2023-03-20T19:29:48Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755268251-FlowBasedTPAttributeValidReadFilter 2023-03-20T19:26:34Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755410715-FastqToSam-Picard 2023-03-20T19:29:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755460507-ReadGroupBlackListReadFilter 2023-03-20T19:26:37Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755737115-FuncotatorDataSourceDownloader 2023-03-20T19:26:41Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755796763-ConvertHeaderlessHadoopBamShardToBam-BETA 2023-03-20T19:26:41Z https://gatk.broadinstitute.org/hc/en-us/articles/13832755843867-MergeSamFiles-Picard 2023-03-20T19:29:53Z https://gatk.broadinstitute.org/hc/en-us/articles/13832764304539-PathSeqScoreSpark 2023-03-20T19:29:54Z https://gatk.broadinstitute.org/hc/en-us/articles/13832764371227-RevertSam-Picard 2023-03-20T19:29:55Z https://gatk.broadinstitute.org/hc/en-us/articles/13832764794139-IntervalOverlapReadFilter 2023-03-20T19:26:50Z https://gatk.broadinstitute.org/hc/en-us/articles/13832764848667-NonZeroReferenceLengthAlignmentReadFilter 2023-03-20T19:26:51Z https://gatk.broadinstitute.org/hc/en-us/articles/13832764902043-RampedHaplotypeCaller-EXPERIMENTAL 2023-03-20T19:29:58Z https://gatk.broadinstitute.org/hc/en-us/articles/13832764954267-GroundTruthReadsBuilder-EXPERIMENTAL 2023-03-20T19:29:58Z https://gatk.broadinstitute.org/hc/en-us/articles/13832765009947-CollectBaseDistributionByCycleSpark-BETA 2023-03-20T19:29:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832765070875-VariantRecalibrator 2023-03-20T19:29:59Z https://gatk.broadinstitute.org/hc/en-us/articles/13832765186203-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2023-03-20T19:30:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832765447067-CycleSkipStatus 2023-03-20T19:26:58Z https://gatk.broadinstitute.org/hc/en-us/articles/13832765503515-UnmarkDuplicates 2023-03-20T19:30:03Z https://gatk.broadinstitute.org/hc/en-us/articles/13832765563163-HmerIndelNuc 2023-03-20T19:27:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832765965851-NonZeroFragmentLengthReadFilter 2023-03-20T19:27:03Z https://gatk.broadinstitute.org/hc/en-us/articles/13832766215707-PileupSpark-BETA 2023-03-20T19:30:07Z https://gatk.broadinstitute.org/hc/en-us/articles/13832766398363-CigarContainsNoNOperator 2023-03-20T19:27:07Z https://gatk.broadinstitute.org/hc/en-us/articles/13832766565403-FilterFuncotations-EXPERIMENTAL 2023-03-20T19:30:08Z https://gatk.broadinstitute.org/hc/en-us/articles/13832766629019-SplitSamByLibrary-Picard 2023-03-20T19:30:09Z https://gatk.broadinstitute.org/hc/en-us/articles/13832766699291-CrosscheckFingerprints-Picard 2023-03-20T19:30:09Z https://gatk.broadinstitute.org/hc/en-us/articles/13832766863259-GenotypeGVCFs 2026-03-16T17:47:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832766922523-TandemRepeat 2023-03-20T19:27:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832767121179-AnalyzeSaturationMutagenesis-BETA 2023-03-20T19:30:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832767180059-AS-QualByDepth 2023-03-20T19:30:13Z https://gatk.broadinstitute.org/hc/en-us/articles/13832767405339-BuildBamIndex-Picard 2023-03-20T19:30:14Z https://gatk.broadinstitute.org/hc/en-us/articles/13832767546011-NotSecondaryAlignmentReadFilter 2023-03-20T19:27:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832767605787-FindMendelianViolations-Picard 2023-03-20T19:30:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832767845915-ReferenceBases 2023-03-20T19:27:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832767900443-IndexFeatureFile 2023-03-20T19:27:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768017947-ValidAlignmentEndReadFilter 2023-03-20T19:30:17Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768150299-FastaReferenceMaker 2023-03-20T19:30:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768209947-QualityScoreDistributionSpark-BETA 2023-03-20T19:30:19Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768298651-AlleleFraction 2023-03-20T19:27:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768418331-OrientationBiasReadCounts 2023-03-20T19:27:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768481947-AssemblyComplexity 2023-03-20T19:27:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768595739-RenameSampleInVcf-Picard 2023-03-20T19:30:21Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768745115-MappingQualityAvailableReadFilter 2023-03-20T19:27:31Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768941851-CollectDuplicateMetrics-Picard 2023-03-20T19:27:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832768992027-CountReadsSpark 2023-03-20T19:30:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769059355-CountBasesSpark 2023-03-20T19:30:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769139611-PrintReadsSpark 2023-03-20T19:30:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769219995-ASEReadCounter 2023-03-20T19:30:25Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769288475-CalibrateDragstrModel 2023-03-20T19:30:26Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769396635-CreateSomaticPanelOfNormals-BETA 2023-10-26T13:07:23Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769528859-GtcToVcf-Picard 2023-03-20T19:27:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769579419-HmerMotifs 2023-03-20T19:27:40Z https://gatk.broadinstitute.org/hc/en-us/articles/13832769617307-CheckTerminatorBlock-Picard 2023-03-20T19:27:41Z https://gatk.broadinstitute.org/hc/en-us/articles/13832772676379-CollectRnaSeqMetrics-Picard 2023-03-20T19:26:42Z https://gatk.broadinstitute.org/hc/en-us/articles/13832772726427-GatherVcfsCloud-BETA 2023-03-20T19:26:43Z https://gatk.broadinstitute.org/hc/en-us/articles/13832772967067-PassesVendorQualityCheckReadFilter 2023-03-20T19:26:46Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773020955-SplitReads 2023-03-20T19:29:56Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773105307-AS-MappingQualityRankSumTest 2023-03-20T19:26:47Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773160091-ReadPosRankSumTest 2023-03-20T19:26:48Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773231003-BaseQuality 2023-03-20T19:26:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773287451-SeqIsStoredReadFilter 2023-03-20T19:26:49Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773657883-PathSeqFilterSpark 2023-03-20T19:30:00Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773767963-SVConcordance-BETA 2023-03-20T19:30:01Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773809179-PlotDenoisedCopyRatios 2024-02-01T05:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773849883-SplitIntervals 2023-03-20T19:30:01Z https://gatk.broadinstitute.org/hc/en-us/articles/13832773915419-FastaAlternateReferenceMaker 2023-03-20T19:30:02Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774200731-StructuralVariationDiscoveryPipelineSpark-BETA 2023-03-20T19:30:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774278555-EvaluateInfoFieldConcordance-BETA 2023-03-20T19:30:04Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774383643-SplitNCigarReads 2023-03-20T19:30:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774541211-JointGermlineCNVSegmentation-BETA 2023-03-20T19:30:05Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774634139-DepthOfCoverage-BETA 2023-03-20T19:30:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774781723-BaseErrorMetric 2023-03-20T19:27:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774824987-ProperlyPairedReadFilter 2023-03-20T19:27:06Z https://gatk.broadinstitute.org/hc/en-us/articles/13832774963483-SplitVcfs-Picard 2023-03-20T19:30:08Z https://gatk.broadinstitute.org/hc/en-us/articles/13832775247515-CNNVariantTrain-EXPERIMENTAL 2023-03-20T19:30:10Z https://gatk.broadinstitute.org/hc/en-us/articles/13832775467291-FindBadGenomicKmersSpark-BETA 2023-03-20T19:30:11Z https://gatk.broadinstitute.org/hc/en-us/articles/13832775517595-AddCommentsToBam-Picard 2023-03-20T19:30:12Z https://gatk.broadinstitute.org/hc/en-us/articles/13832775704731-AS-BaseQualityRankSumTest 2023-03-20T19:27:15Z https://gatk.broadinstitute.org/hc/en-us/articles/13832775764123-Concordance 2023-03-20T19:30:13Z https://gatk.broadinstitute.org/hc/en-us/articles/13832775836955-FragmentLengthReadFilter 2023-03-20T19:27:16Z https://gatk.broadinstitute.org/hc/en-us/articles/13832775967259-CollectRrbsMetrics-Picard 2023-03-20T19:27:18Z https://gatk.broadinstitute.org/hc/en-us/articles/13832776160539-WgsMetricsWithNonZeroCoverage 2023-03-20T19:27:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832776236443-IndelErrorMetric 2023-03-20T19:27:20Z https://gatk.broadinstitute.org/hc/en-us/articles/13832776296859-ShiftFasta-BETA 2023-03-20T19:30:16Z https://gatk.broadinstitute.org/hc/en-us/articles/13832776470427-MetricsReadFilter 2023-03-20T19:27:23Z https://gatk.broadinstitute.org/hc/en-us/articles/13832776614555-FingerprintingDetailMetrics 2023-03-20T19:27:24Z https://gatk.broadinstitute.org/hc/en-us/articles/13832776768795-DepthPerSampleHC 2023-03-20T19:27:26Z https://gatk.broadinstitute.org/hc/en-us/articles/13832776864923-ConvertSequencingArtifactToOxoG-Picard 2023-03-20T19:27:28Z https://gatk.broadinstitute.org/hc/en-us/articles/13832777015195-CountNs 2023-03-20T19:27:29Z https://gatk.broadinstitute.org/hc/en-us/articles/13832777134619-ReadAnonymizer-EXPERIMENTAL 2023-03-20T19:30:22Z https://gatk.broadinstitute.org/hc/en-us/articles/13832777254555-CollectOxoGMetrics-Picard 2023-03-20T19:27:32Z https://gatk.broadinstitute.org/hc/en-us/articles/13832777338267-CreateReadCountPanelOfNormals 2023-03-20T19:27:33Z https://gatk.broadinstitute.org/hc/en-us/articles/13832777777179-FilterVariantTranches 2023-03-20T19:30:26Z https://gatk.broadinstitute.org/hc/en-us/articles/13832777893403-CheckPileup 2023-03-20T19:30:27Z https://gatk.broadinstitute.org/hc/en-us/articles/13832778101659-ReadLengthReadFilter 2023-03-20T19:27:42Z https://gatk.broadinstitute.org/hc/en-us/articles/13832778146203-CleanSam-Picard 2023-03-20T19:27:42Z https://gatk.broadinstitute.org/hc/en-us/articles/16334400824347-Upcoming-GATK-Workshop-in-Gujarat-India-Jan-17-19-2024 2023-07-17T18:08:20Z https://gatk.broadinstitute.org/hc/en-us/articles/16334676883483-Upcoming-GATK-Workshop-in-San-Pedro-Costa-Rica-Feb-5-8-2024 2023-10-06T03:26:22Z https://gatk.broadinstitute.org/hc/en-us/articles/16334710058267-Upcoming-GATK-Workshop-in-Granada-Spain-Nov-13-16-2023 2023-07-17T18:13:54Z https://gatk.broadinstitute.org/hc/en-us/articles/16334781122203-Upcoming-GATK-Workshop-in-Taipei-Taiwan-Nov-13-16-2023 2023-09-20T13:50:18Z https://gatk.broadinstitute.org/hc/en-us/articles/16957867036315-Introducing-GATK-Biggest-Practices-for-Joint-Calling-Supersized-Cohorts 2025-08-25T19:07:42Z https://gatk.broadinstitute.org/hc/en-us/articles/17295731870235-Masked-reference-genomes 2024-11-01T16:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/18440261559195-Joint-Calling-and-the-Batch-Effect-Boogeyman 2023-10-31T14:30:24Z https://gatk.broadinstitute.org/hc/en-us/articles/18440923786907-Who-s-Not-Afraid-of-the-Batch-Effect-Boogeyman 2024-11-09T18:20:09Z https://gatk.broadinstitute.org/hc/en-us/articles/18965297287067-How-to-setup-and-use-temporary-folder-for-GATK-local-execution 2025-09-15T15:11:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21904919804699-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2024-01-09T19:44:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21904919894171-ChromosomeCounts 2024-01-09T19:37:58Z https://gatk.broadinstitute.org/hc/en-us/articles/21904920211227-MeanQualityByCycle-Picard 2024-01-09T19:44:02Z https://gatk.broadinstitute.org/hc/en-us/articles/21904920344219-GenotypeConcordance-Picard 2024-01-09T19:44:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21904927714843-LibraryReadFilter 2024-01-09T19:37:59Z https://gatk.broadinstitute.org/hc/en-us/articles/21904927922971-NonChimericOriginalAlignmentReadFilter 2024-01-09T19:38:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21904928322075-BwaMemIndexImageCreator 2024-01-09T19:44:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21904928389787-VerifyIDIntensityContaminationMetrics 2024-01-09T19:44:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21904928462107-NotProperlyPairedReadFilter 2024-01-09T19:38:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21904928773403-SampleReadFilter 2024-01-09T19:38:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21904936401947-CollectQualityYieldMetrics-Picard 2024-01-09T19:38:14Z https://gatk.broadinstitute.org/hc/en-us/articles/21904948391067-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2024-01-09T19:38:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21904949322523-AnalyzeCovariates 2024-01-09T19:44:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21904949988891-SecondOfPairReadFilter 2024-01-09T19:38:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21904950163227-AS-StrandOddsRatio 2024-01-09T19:38:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21904951112091-GnarlyGenotyper-BETA 2024-01-09T19:44:16Z https://gatk.broadinstitute.org/hc/en-us/articles/21904951531675-AnnotateVcfWithExpectedAlleleFraction 2024-01-09T19:44:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21904951722395-CountVariants 2024-01-09T19:44:20Z https://gatk.broadinstitute.org/hc/en-us/articles/21904952170907-VariantCallingSummaryMetrics 2024-01-09T19:44:22Z https://gatk.broadinstitute.org/hc/en-us/articles/21904952336795-ArraysControlCodesSummaryMetrics 2024-01-09T19:44:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21904952392859-VariantAnnotator 2024-01-09T19:44:24Z https://gatk.broadinstitute.org/hc/en-us/articles/21904952624283-PrimaryLineReadFilter 2024-01-09T19:38:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21904953093659-MendelianViolationMetrics 2024-01-09T19:44:28Z https://gatk.broadinstitute.org/hc/en-us/articles/21904953715355-FlowFeatureMapper-EXPERIMENTAL 2024-01-09T19:44:32Z https://gatk.broadinstitute.org/hc/en-us/articles/21904953853595-VariantsToTable 2024-06-26T09:36:54Z https://gatk.broadinstitute.org/hc/en-us/articles/21904958169243-DumpTabixIndex 2024-01-09T19:38:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21904958481819-CollectHiSeqXPfFailMetrics-Picard 2024-01-09T19:38:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21904959027227-ExcessiveEndClippedReadFilter 2024-01-09T19:38:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21904960413595-FilterVcf-Picard 2024-01-09T19:38:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21904960817563-CountReads 2024-01-09T19:44:14Z https://gatk.broadinstitute.org/hc/en-us/articles/21904962123035-BaseDistributionByCycleMetrics 2024-01-09T19:44:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21904962829083-BarcodeMetric 2024-01-09T19:44:06Z https://gatk.broadinstitute.org/hc/en-us/articles/21904963274651-FirstOfPairReadFilter 2024-01-09T19:38:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21904963716635-CalcMetadataSpark-BETA 2024-01-09T19:44:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21904964615451-CollectHsMetrics-Picard 2024-01-09T19:44:15Z https://gatk.broadinstitute.org/hc/en-us/articles/21904964800411-IlluminaBasecallingMetrics 2024-01-09T19:44:16Z https://gatk.broadinstitute.org/hc/en-us/articles/21904965033883-EstimateLibraryComplexity-Picard 2024-01-09T19:38:29Z https://gatk.broadinstitute.org/hc/en-us/articles/21904965573147-AllowAllReadsReadFilter 2024-01-09T19:38:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21904965707675-NotDuplicateReadFilter 2024-01-09T19:38:37Z https://gatk.broadinstitute.org/hc/en-us/articles/21904965818267-OverlappingErrorMetric 2024-01-09T19:44:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21904966037275-PreAdapterSummaryMetrics 2024-01-09T19:44:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21904966313755-MergePedIntoVcf-Picard 2024-01-09T19:38:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21904966705563-CountBases 2024-01-09T19:44:27Z https://gatk.broadinstitute.org/hc/en-us/articles/21904967347995-MappingQuality 2024-01-09T19:38:54Z https://gatk.broadinstitute.org/hc/en-us/articles/21904967427227-QualByDepth 2024-01-09T19:38:55Z https://gatk.broadinstitute.org/hc/en-us/articles/21904967930651-AS-RMSMappingQuality 2024-01-09T19:39:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21904968017947-PFFailSummaryMetric 2024-01-09T19:44:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21904968151707-CountVariantsSpark 2024-01-09T19:39:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21904968342171-IlluminaBasecallsToFastq-Picard 2024-01-09T19:39:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21904968408091-SamFormatConverter-Picard 2024-01-09T19:39:06Z https://gatk.broadinstitute.org/hc/en-us/articles/21904968607643-FisherStrand 2024-01-09T19:39:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21904968768539-ClusterCrosscheckMetrics-Picard 2024-01-09T19:39:09Z https://gatk.broadinstitute.org/hc/en-us/articles/21904969078171-SoftClippedReadFilter 2024-01-09T19:39:13Z https://gatk.broadinstitute.org/hc/en-us/articles/21904969545499-DepthPerAlleleBySample 2024-01-09T19:39:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21904970029467-FuncotateSegments-BETA 2024-01-09T19:44:47Z https://gatk.broadinstitute.org/hc/en-us/articles/21904970604059-BwaSpark-BETA 2024-01-09T19:44:49Z https://gatk.broadinstitute.org/hc/en-us/articles/21904970745243-Pileup 2024-01-09T19:44:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21904970806171-OverclippedReadFilter 2024-01-09T19:38:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21904971233435-WellformedReadFilter 2024-01-09T19:44:06Z https://gatk.broadinstitute.org/hc/en-us/articles/21904971708699-Funcotator 2024-01-09T19:44:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21904971999387-PathSeqPipelineSpark 2024-01-09T19:44:09Z https://gatk.broadinstitute.org/hc/en-us/articles/21904972266779-AlignmentAgreesWithHeaderReadFilter 2024-01-09T19:38:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21904972581787-VariantEval-BETA 2024-01-09T19:38:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21904972669339-GcBiasSummaryMetrics 2024-01-09T19:44:13Z https://gatk.broadinstitute.org/hc/en-us/articles/21904972745371-RnaSeqMetrics 2024-01-09T19:44:13Z https://gatk.broadinstitute.org/hc/en-us/articles/21904972894875-FixVcfHeader-Picard 2024-01-09T19:44:14Z https://gatk.broadinstitute.org/hc/en-us/articles/21904973380891-JumpingLibraryMetrics 2024-01-09T19:44:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21904973656475-ViewSam-Picard 2024-01-09T19:44:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21904974967963-BafRegressMetrics 2024-01-09T19:44:25Z https://gatk.broadinstitute.org/hc/en-us/articles/21904975253275-StrandOddsRatio 2024-01-09T19:38:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21904976232859-AlleleFrequencyQCMetric 2024-01-09T19:44:33Z https://gatk.broadinstitute.org/hc/en-us/articles/21904976896411-UpdateVCFSequenceDictionary 2024-01-09T19:44:36Z https://gatk.broadinstitute.org/hc/en-us/articles/21904977669915-ReadGroupHasFlowOrderReadFilter 2024-01-09T19:39:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21904978383387-SetNmMdAndUqTags-Picard 2024-01-09T19:44:45Z https://gatk.broadinstitute.org/hc/en-us/articles/21904978930459-CalculateFingerprintMetrics-Picard 2025-11-03T18:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/21904979290779-RMSMappingQuality 2024-01-09T19:38:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21904980248603-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2024-01-09T19:44:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21904980836507-AccumulateQualityYieldMetrics-Picard 2024-01-09T19:38:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21904981307547-PrintReadsHeader 2024-01-09T19:44:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21904982117787-BamToBfq-Picard 2024-01-09T19:38:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21904982473499-FilterSamReads-Picard 2024-01-09T19:44:24Z https://gatk.broadinstitute.org/hc/en-us/articles/21904982885275-CompareReferences-EXPERIMENTAL 2024-01-09T19:44:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21904983403931-DetermineGermlineContigPloidy 2024-01-09T19:38:52Z https://gatk.broadinstitute.org/hc/en-us/articles/21904983490715-FindBreakpointEvidenceSpark-BETA 2024-01-09T19:44:30Z https://gatk.broadinstitute.org/hc/en-us/articles/21904983565595-UniqueAltReadCount 2024-01-09T19:38:53Z https://gatk.broadinstitute.org/hc/en-us/articles/21904984396315-CNNVariantWriteTensors-EXPERIMENTAL 2024-01-09T19:44:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21904984799387-PostProcessReadsForRSEM-BETA 2024-01-09T19:44:38Z https://gatk.broadinstitute.org/hc/en-us/articles/21904985283739-CollectSamErrorMetrics-Picard 2024-01-09T19:39:11Z https://gatk.broadinstitute.org/hc/en-us/articles/21904985710875-SiteDepthtoBAF-EXPERIMENTAL 2024-01-09T19:44:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21904986220827-CompareMetrics-Picard 2024-01-09T19:44:46Z https://gatk.broadinstitute.org/hc/en-us/articles/21904986436635-GatherBamFiles-Picard 2024-01-09T19:39:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21904986675995-PathSeqBuildReferenceTaxonomy 2024-01-09T19:39:25Z https://gatk.broadinstitute.org/hc/en-us/articles/21904987074587-CollectAlignmentSummaryMetrics-Picard 2024-01-09T19:39:29Z https://gatk.broadinstitute.org/hc/en-us/articles/21904987153819-AnnotateVcfWithBamDepth 2024-01-09T19:44:51Z https://gatk.broadinstitute.org/hc/en-us/articles/21904988677147-ErrorMetric 2024-01-09T19:44:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21904988946587-LiftOverIntervalList-Picard 2024-01-09T19:38:36Z https://gatk.broadinstitute.org/hc/en-us/articles/21904989937435-CollectMultipleMetricsSpark-BETA 2024-01-09T19:44:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21904990314651-CheckFingerprint-Picard 2024-01-09T19:38:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21904992595355-ClipReads 2024-01-09T19:44:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21904993019419-GetSampleName 2024-01-09T19:44:42Z https://gatk.broadinstitute.org/hc/en-us/articles/21904993091611-CollectSVEvidence-BETA 2024-01-09T19:44:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21904993427611-CalculateReadGroupChecksum-Picard 2024-01-09T19:44:45Z https://gatk.broadinstitute.org/hc/en-us/articles/21904993501467-HaplotypeFilteringAnnotation 2024-01-09T19:39:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21904993968923-BaitBiasSummaryMetrics 2024-01-09T19:44:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21904996835867--Tool-Documentation-Index 2024-01-23T10:45:22Z https://gatk.broadinstitute.org/hc/en-us/articles/21904997025435-HasReadGroupReadFilter 2024-01-09T19:38:51Z https://gatk.broadinstitute.org/hc/en-us/articles/21904997621787-FlowBasedTPAttributeSymetricReadFilter 2024-01-09T19:38:57Z https://gatk.broadinstitute.org/hc/en-us/articles/21904997855643-HaplotypeBasedVariantRecaller-EXPERIMENTAL 2024-01-09T19:44:34Z https://gatk.broadinstitute.org/hc/en-us/articles/21904998718619-GeneExpressionEvaluation-BETA 2024-01-09T19:44:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21904998954139-PSFilterMetrics 2024-01-09T19:44:40Z https://gatk.broadinstitute.org/hc/en-us/articles/21904999597979-MarkDuplicatesSpark 2024-01-09T19:44:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21904999933211-GcBiasMetrics 2024-01-09T19:44:46Z https://gatk.broadinstitute.org/hc/en-us/articles/21905000513051-AS-FisherStrand 2024-01-09T19:39:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21905001216411-GatherVcfs-Picard 2024-01-09T19:39:32Z https://gatk.broadinstitute.org/hc/en-us/articles/21905001435419-MarkDuplicatesWithMateCigar-Picard 2024-01-09T19:44:53Z https://gatk.broadinstitute.org/hc/en-us/articles/21905002317339-LearnReadOrientationModel 2024-01-09T19:39:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21905002382235-CollectReadCounts 2024-01-09T19:44:58Z https://gatk.broadinstitute.org/hc/en-us/articles/21905002769051-MappingQualityNotZeroReadFilter 2024-01-09T19:39:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21905003274779-ComposeSTRTableFile 2024-01-09T19:45:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21905003341595-MateDifferentStrandReadFilter 2024-01-09T19:45:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21905003544475-FingerprintMetrics 2024-01-09T19:45:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21905003676955-BaitBiasDetailMetrics 2024-01-09T19:45:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21905004390299-NormalizeFasta-Picard 2024-01-09T19:44:34Z https://gatk.broadinstitute.org/hc/en-us/articles/21905007031579-CompareBaseQualities 2024-01-09T19:39:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21905007191835-SamComparisonMetric 2024-01-09T19:44:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905007647643-MappedReadFilter 2024-01-09T19:39:33Z https://gatk.broadinstitute.org/hc/en-us/articles/21905008166427-PathSeqBuildKmers 2024-01-09T19:44:55Z https://gatk.broadinstitute.org/hc/en-us/articles/21905009596187-FilterMutectCalls 2024-01-09T19:45:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21905009929755-SelectVariants 2024-01-09T19:45:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21905010266779-ScoreVariantAnnotations-BETA 2024-01-09T19:45:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21905011533467-ValidAlignmentStartReadFilter 2024-01-09T19:45:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905012323227-VcfToIntervalList-Picard 2024-01-09T19:45:22Z https://gatk.broadinstitute.org/hc/en-us/articles/21905012419611-SetNmAndUqTags-Picard 2024-01-09T19:45:22Z https://gatk.broadinstitute.org/hc/en-us/articles/21905012592411-MarkIlluminaAdapters-Picard 2024-01-09T19:45:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21905012667419-SampleList 2024-01-09T19:40:27Z https://gatk.broadinstitute.org/hc/en-us/articles/21905013146395-CollectSequencingArtifactMetrics-Picard 2024-01-09T19:39:31Z https://gatk.broadinstitute.org/hc/en-us/articles/21905013222811-GenotypeConcordanceContingencyMetrics 2024-01-09T19:44:52Z https://gatk.broadinstitute.org/hc/en-us/articles/21905014213019-FragmentDepthPerAlleleBySample 2024-01-09T19:39:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21905014552603-MappingQualityRankSumTest 2024-01-09T19:39:47Z https://gatk.broadinstitute.org/hc/en-us/articles/21905014706971-GetNormalArtifactData 2024-01-09T19:45:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21905018843035-CheckIlluminaDirectory-Picard 2024-01-09T19:45:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21905019550235-FixMisencodedBaseQualityReads 2024-01-09T19:45:30Z https://gatk.broadinstitute.org/hc/en-us/articles/21905020571419-CompareDuplicatesSpark-BETA 2024-01-09T19:45:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21905020645275-CollectRawWgsMetrics-Picard 2024-01-09T19:45:36Z https://gatk.broadinstitute.org/hc/en-us/articles/21905021593243-ExtractSequences-Picard 2024-01-09T19:44:53Z https://gatk.broadinstitute.org/hc/en-us/articles/21905021727515-GatherBQSRReports 2024-01-09T19:39:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21905021795739-CalculateContamination 2024-03-27T20:38:20Z https://gatk.broadinstitute.org/hc/en-us/articles/21905022245531-IntervalListTools-Picard 2024-01-09T19:44:56Z https://gatk.broadinstitute.org/hc/en-us/articles/21905022322587-CollectInsertSizeMetrics-Picard 2024-01-09T19:39:41Z https://gatk.broadinstitute.org/hc/en-us/articles/21905022651803-SortSamSpark-BETA 2024-01-09T19:44:59Z https://gatk.broadinstitute.org/hc/en-us/articles/21905023129627-CollectJumpingLibraryMetrics-Picard 2024-01-09T19:39:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905023287835-HsMetrics 2024-01-09T19:45:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21905023522843-NonNFastaSize-Picard 2024-01-09T19:45:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21905024047771-IlluminaBasecallsToSam-Picard 2024-01-09T19:40:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21905024529435-PlatformUnitReadFilter 2024-01-09T19:40:06Z https://gatk.broadinstitute.org/hc/en-us/articles/21905024896411-CreateHadoopBamSplittingIndex-BETA 2024-01-09T19:40:09Z https://gatk.broadinstitute.org/hc/en-us/articles/21905025322523-HaplotypeCaller 2024-01-09T19:45:16Z https://gatk.broadinstitute.org/hc/en-us/articles/21905025789723-CountFalsePositives-BETA 2024-01-09T19:45:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905025890075-MateUnmappedAndUnmappedReadFilter 2024-01-09T19:40:20Z https://gatk.broadinstitute.org/hc/en-us/articles/21905025960987-CollectIlluminaLaneMetrics-Picard 2024-01-09T19:40:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21905026847643-FragmentLength 2024-01-09T19:40:30Z https://gatk.broadinstitute.org/hc/en-us/articles/21905027236123-ReblockGVCF 2024-01-09T19:45:28Z https://gatk.broadinstitute.org/hc/en-us/articles/21905027821851-FeaturizedReadSets 2024-01-09T19:40:40Z https://gatk.broadinstitute.org/hc/en-us/articles/21905028015003-RevertSamSpark-BETA 2024-01-09T19:45:32Z https://gatk.broadinstitute.org/hc/en-us/articles/21905029048859-GcContent 2024-01-09T19:40:52Z https://gatk.broadinstitute.org/hc/en-us/articles/21905029173147-VcfToAdpc-Picard 2024-01-09T19:40:53Z https://gatk.broadinstitute.org/hc/en-us/articles/21905029259547-GoodCigarReadFilter 2024-01-09T19:40:54Z https://gatk.broadinstitute.org/hc/en-us/articles/21905029341083-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2024-01-09T19:40:55Z https://gatk.broadinstitute.org/hc/en-us/articles/21905029737627-LeftAlignIndels 2024-01-09T19:44:59Z https://gatk.broadinstitute.org/hc/en-us/articles/21905029809051-FilterIntervals 2024-01-09T19:39:46Z https://gatk.broadinstitute.org/hc/en-us/articles/21905030104219-HaplotypeCallerSpark-BETA 2024-01-09T19:45:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21905030271259-SplitSamByNumberOfReads-Picard 2024-01-09T19:45:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21905030826395-BaseRecalibratorSpark-BETA 2024-01-09T19:45:06Z https://gatk.broadinstitute.org/hc/en-us/articles/21905030951963-CalculateMixingFractions 2024-01-09T19:45:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21905031120667-AccumulateVariantCallingMetrics-Picard 2024-01-09T19:39:59Z https://gatk.broadinstitute.org/hc/en-us/articles/21905031297179-SVCluster-BETA 2024-01-09T19:45:09Z https://gatk.broadinstitute.org/hc/en-us/articles/21905031424411-ReadGroupReadFilter 2024-01-09T19:40:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21905031474459-MappingQualityReadFilter 2024-01-09T19:45:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21905031525019-GenomicsDBImport 2024-01-09T19:45:11Z https://gatk.broadinstitute.org/hc/en-us/articles/21905031868571-CreateBafRegressMetricsFile-Picard 2024-01-09T19:40:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21905031936667-RawGtCount 2024-01-09T19:40:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21905032147995-PrintReads 2024-01-09T19:45:14Z https://gatk.broadinstitute.org/hc/en-us/articles/21905032214427-GenotypeConcordanceSummaryMetrics 2024-01-09T19:45:14Z https://gatk.broadinstitute.org/hc/en-us/articles/21905032288667-HmerQualitySymetricReadFilter 2024-01-09T19:40:11Z https://gatk.broadinstitute.org/hc/en-us/articles/21905032458651-MateDistantReadFilter 2024-01-09T19:45:16Z https://gatk.broadinstitute.org/hc/en-us/articles/21905033373083-ClusteredCrosscheckMetric 2024-01-09T19:45:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21905033439643-JexlExpressionReadTagValueFilter 2024-01-09T19:40:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21905033876251-MatchingBasesAndQualsReadFilter 2024-01-09T19:40:28Z https://gatk.broadinstitute.org/hc/en-us/articles/21905033935515-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2024-01-09T19:45:24Z https://gatk.broadinstitute.org/hc/en-us/articles/21905035013531-ModelSegments 2024-01-09T19:45:31Z https://gatk.broadinstitute.org/hc/en-us/articles/21905035467035-AmbiguousBaseReadFilter 2024-01-09T19:40:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21905035634459-RemoveNearbyIndels 2024-01-09T19:45:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21905036102043-MarkDuplicates-Picard 2024-01-09T19:40:51Z https://gatk.broadinstitute.org/hc/en-us/articles/21905036854555-PreAdapterDetailMetrics 2024-01-09T19:45:41Z https://gatk.broadinstitute.org/hc/en-us/articles/21905037286427-PSScoreMetrics 2024-01-09T19:45:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21905037520923-FilterAlignmentArtifacts-EXPERIMENTAL 2024-01-09T19:45:45Z https://gatk.broadinstitute.org/hc/en-us/articles/21905038144155-ApplyBQSR 2024-01-09T19:44:54Z https://gatk.broadinstitute.org/hc/en-us/articles/21905038231579-CpxVariantReInterpreterSpark-BETA 2024-01-09T19:44:55Z https://gatk.broadinstitute.org/hc/en-us/articles/21905038459035-MakeSitesOnlyVcf-Picard 2024-01-09T19:44:56Z https://gatk.broadinstitute.org/hc/en-us/articles/21905038684571-StrandBiasBySample 2024-01-09T19:39:42Z https://gatk.broadinstitute.org/hc/en-us/articles/21905041649691-AlignmentSummaryMetrics 2024-01-09T19:45:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905041859227-ReadsPipelineSpark-BETA 2024-01-09T19:45:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905043722523-RrbsCpgDetailMetrics 2024-01-09T19:45:28Z https://gatk.broadinstitute.org/hc/en-us/articles/21905044109467-LeftAlignAndTrimVariants 2024-01-09T19:45:30Z https://gatk.broadinstitute.org/hc/en-us/articles/21905044430235-DuplicationMetrics 2024-01-09T19:45:32Z https://gatk.broadinstitute.org/hc/en-us/articles/21905044859419-BedToIntervalList-Picard 2024-01-09T19:45:34Z https://gatk.broadinstitute.org/hc/en-us/articles/21905045323035-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2024-01-09T19:45:36Z https://gatk.broadinstitute.org/hc/en-us/articles/21905046146971-PositionBasedDownsampleSam-Picard 2024-01-09T19:40:58Z https://gatk.broadinstitute.org/hc/en-us/articles/21905046817691-RrbsSummaryMetrics 2024-01-09T19:45:27Z https://gatk.broadinstitute.org/hc/en-us/articles/21905047102875-TrainVariantAnnotationsModel-BETA 2024-01-09T19:45:29Z https://gatk.broadinstitute.org/hc/en-us/articles/21905047868699-PFFailDetailedMetric 2024-01-09T19:45:33Z https://gatk.broadinstitute.org/hc/en-us/articles/21905049074843-AllelePseudoDepth 2024-01-09T19:40:56Z https://gatk.broadinstitute.org/hc/en-us/articles/21905049228315-TransmittedSingleton 2024-01-09T19:40:57Z https://gatk.broadinstitute.org/hc/en-us/articles/21905050144027-CollectWgsMetrics-Picard 2024-01-09T19:41:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21905050711963-LikelihoodRankSumTest 2024-01-09T19:41:13Z https://gatk.broadinstitute.org/hc/en-us/articles/21905050792603-BaseRecalibrator 2024-01-09T19:45:49Z https://gatk.broadinstitute.org/hc/en-us/articles/21905050876187-RevertBaseQualityScores 2024-01-09T19:45:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905051205787-ClippingRankSumTest 2024-01-09T19:41:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905051324699-VariantCallingDetailMetrics 2024-01-09T19:45:52Z https://gatk.broadinstitute.org/hc/en-us/articles/21905052461211-ApplyVQSR 2024-01-09T19:45:58Z https://gatk.broadinstitute.org/hc/en-us/articles/21905053277211-AS-InbreedingCoeff 2024-01-09T19:41:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21905053774363-SVAnnotate 2024-01-09T19:46:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21905054147483-PlotModeledSegments 2024-01-09T19:41:49Z https://gatk.broadinstitute.org/hc/en-us/articles/21905054376859-CombineGVCFs 2024-01-09T19:46:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21905054580251-CollectGcBiasMetrics-Picard 2024-01-09T19:41:54Z https://gatk.broadinstitute.org/hc/en-us/articles/21905054752411-CollectQualityYieldMetricsSpark-BETA 2024-01-09T19:45:11Z https://gatk.broadinstitute.org/hc/en-us/articles/21905054915739-FlowPairHMMAlignReadsToHaplotypes-EXPERIMENTAL 2024-01-09T19:45:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21905055509531-BwaAndMarkDuplicatesPipelineSpark-BETA 2024-01-09T19:45:15Z https://gatk.broadinstitute.org/hc/en-us/articles/21905056067867-ReplaceSamHeader-Picard 2024-01-09T19:45:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905056430235-CountBasesInReference 2024-01-09T19:45:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21905056798491-PathSeqBwaSpark 2024-01-09T19:45:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21905057155995-MeanQualityByCycleSpark-BETA 2024-01-09T19:45:25Z https://gatk.broadinstitute.org/hc/en-us/articles/21905057379739-CollectTargetedPcrMetrics-Picard 2024-01-09T19:45:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21905057447323-CollectBaseDistributionByCycle-Picard 2024-01-09T19:40:32Z https://gatk.broadinstitute.org/hc/en-us/articles/21905057898523-MergeBamAlignment-Picard 2024-01-09T19:40:37Z https://gatk.broadinstitute.org/hc/en-us/articles/21905058509723-ExtractIlluminaBarcodes-Picard 2024-01-09T19:40:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21905059048731-HmerIndelLength 2024-01-09T19:40:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21905059210907-OriginalAlignment 2024-01-09T19:40:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905059452187-CreateSequenceDictionary-Picard 2024-01-09T19:45:38Z https://gatk.broadinstitute.org/hc/en-us/articles/21905060964251-UmiMetrics 2024-01-09T19:45:46Z https://gatk.broadinstitute.org/hc/en-us/articles/21905061105563-AS-ReadPosRankSumTest 2024-01-09T19:41:09Z https://gatk.broadinstitute.org/hc/en-us/articles/21905061980827-DownsampleSam-Picard 2024-01-09T19:45:51Z https://gatk.broadinstitute.org/hc/en-us/articles/21905062525723-ArraysVariantCallingDetailMetrics 2024-01-09T19:45:54Z https://gatk.broadinstitute.org/hc/en-us/articles/21905063212187-CheckReferenceCompatibility-EXPERIMENTAL 2024-01-09T19:45:41Z https://gatk.broadinstitute.org/hc/en-us/articles/21905064081563-PairedReadFilter 2024-01-09T19:41:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21905065299227-BQSRPipelineSpark-BETA 2024-01-09T19:45:53Z https://gatk.broadinstitute.org/hc/en-us/articles/21905065755803-CollectInsertSizeMetricsSpark-BETA 2024-01-09T19:45:55Z https://gatk.broadinstitute.org/hc/en-us/articles/21905065906715-DenoiseReadCounts 2024-01-09T19:41:28Z https://gatk.broadinstitute.org/hc/en-us/articles/21905066509595-ReadNameReadFilter 2024-01-09T19:41:34Z https://gatk.broadinstitute.org/hc/en-us/articles/21905066736795-ErrorSummaryMetrics 2024-01-09T19:46:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21905067694491-VcfFormatConverter-Picard 2024-01-09T19:46:06Z https://gatk.broadinstitute.org/hc/en-us/articles/21905068340507-LiftoverVcf-Picard 2024-01-09T19:46:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21905068973851-ApplyBQSRSpark-BETA 2024-01-09T19:46:13Z https://gatk.broadinstitute.org/hc/en-us/articles/21905070123035-MethylationTypeCaller-EXPERIMENTAL 2024-01-09T19:46:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905070238235-FingerprintingSummaryMetrics 2024-01-09T19:46:20Z https://gatk.broadinstitute.org/hc/en-us/articles/21905071101211-ReadLengthEqualsCigarLengthReadFilter 2024-01-09T19:46:24Z https://gatk.broadinstitute.org/hc/en-us/articles/21905072427035-PostprocessGermlineCNVCalls 2024-01-09T19:45:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21905072637595-GenotypeSummaries 2024-01-09T19:41:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21905072711195-FlagStatSpark 2024-01-09T19:45:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21905074591387-IndelClassify 2024-01-09T19:41:25Z https://gatk.broadinstitute.org/hc/en-us/articles/21905074980507-BaseQualityRankSumTest 2024-01-09T19:41:29Z https://gatk.broadinstitute.org/hc/en-us/articles/21905075548443-ExtractVariantAnnotations-BETA 2024-01-09T19:46:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21905075857307-ScatterIntervalsByNs-Picard 2024-01-09T19:46:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21905076343067-CollectArraysVariantCallingMetrics-Picard 2024-01-09T19:46:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21905076749595-AddOrReplaceReadGroups-Picard 2024-01-09T19:41:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21905077623451-ReadTagValueFilter 2024-01-09T19:41:57Z https://gatk.broadinstitute.org/hc/en-us/articles/21905078265627-CalculateGenotypePosteriors 2024-01-09T19:46:14Z https://gatk.broadinstitute.org/hc/en-us/articles/21905078487067-WellformedFlowBasedReadFilter 2024-01-09T19:46:16Z https://gatk.broadinstitute.org/hc/en-us/articles/21905078887707-CNNScoreVariants 2024-01-09T19:46:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905079030427-CpcgMetrics 2024-01-09T19:46:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905079522459-PrintDistantMates 2024-01-09T19:46:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21905079989147-ReorderSam-Picard 2024-01-09T19:41:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21905080070427-RawWgsMetrics 2024-01-09T19:45:42Z https://gatk.broadinstitute.org/hc/en-us/articles/21905080207899-NotSupplementaryAlignmentReadFilter 2024-01-09T19:41:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21905080913947-GetPileupSummaries 2024-01-09T19:45:47Z https://gatk.broadinstitute.org/hc/en-us/articles/21905080999195-FifoBuffer-Picard 2024-01-09T19:41:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21905081064475-ExcessHet 2024-01-09T19:41:11Z https://gatk.broadinstitute.org/hc/en-us/articles/21905081124891-VariantFiltration 2024-01-09T19:45:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21905081472795-GenotypeConcordanceDetailMetrics 2024-01-09T19:45:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905081560347-GatherTranches-BETA 2024-01-09T19:41:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905081889563-CompareSAMs-Picard 2024-01-09T19:45:52Z https://gatk.broadinstitute.org/hc/en-us/articles/21905082214811-TransferReadTags-EXPERIMENTAL 2024-01-09T19:45:54Z https://gatk.broadinstitute.org/hc/en-us/articles/21905082371355-PossibleDeNovo 2024-03-06T02:59:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21905082550171-GroundTruthScorer-EXPERIMENTAL 2024-01-09T19:45:56Z https://gatk.broadinstitute.org/hc/en-us/articles/21905083347227-MappingQualityZero 2024-01-09T19:41:36Z https://gatk.broadinstitute.org/hc/en-us/articles/21905083931035-Mutect2 2024-01-09T19:46:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21905084860699-LocalAssembler-BETA 2024-01-09T19:46:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21905085664155-TargetedPcrMetrics 2024-01-09T19:46:13Z https://gatk.broadinstitute.org/hc/en-us/articles/21905086033051-MergeVcfs-Picard 2024-01-09T19:46:15Z https://gatk.broadinstitute.org/hc/en-us/articles/21905086099611-CollectMultipleMetrics-Picard 2024-01-09T19:46:15Z https://gatk.broadinstitute.org/hc/en-us/articles/21905086390811-ExtractSVEvidenceSpark-BETA 2024-01-09T19:46:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905086995867-PreprocessIntervals 2024-01-09T19:46:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21905087790619-SortVcf-Picard 2024-01-09T19:46:25Z https://gatk.broadinstitute.org/hc/en-us/articles/21905089485851-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2024-01-09T19:45:53Z https://gatk.broadinstitute.org/hc/en-us/articles/21905090485659-GermlineCNVCaller 2024-01-09T19:41:33Z https://gatk.broadinstitute.org/hc/en-us/articles/21905090568347-UpdateVcfSequenceDictionary-Picard 2024-01-09T19:41:33Z https://gatk.broadinstitute.org/hc/en-us/articles/21905091185563-PlatformReadFilter 2024-01-09T19:41:40Z https://gatk.broadinstitute.org/hc/en-us/articles/21905092095771-CollectVariantCallingMetrics-Picard 2024-01-09T19:41:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905092375707-PrintReadCounts-EXPERIMENTAL 2024-01-09T19:46:09Z https://gatk.broadinstitute.org/hc/en-us/articles/21905092647579-ArraysVariantCallingSummaryMetrics 2024-01-09T19:46:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21905092788635-AddOATag-Picard 2024-01-09T19:46:11Z https://gatk.broadinstitute.org/hc/en-us/articles/21905092988059-MateOnSameContigOrNoMappedMateReadFilter 2024-01-09T19:46:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21905093071515-Coverage 2024-01-09T19:42:00Z https://gatk.broadinstitute.org/hc/en-us/articles/21905094088475-CollectAllelicCounts 2024-01-09T19:46:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905094273947-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2024-01-09T19:42:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21905095539867-FixMateInformation-Picard 2024-01-09T19:42:24Z https://gatk.broadinstitute.org/hc/en-us/articles/21905096293019-WgsMetrics 2024-01-09T19:46:29Z https://gatk.broadinstitute.org/hc/en-us/articles/21905096771483-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2024-01-09T19:45:57Z https://gatk.broadinstitute.org/hc/en-us/articles/21905096836763-IntervalListToBed-Picard 2024-01-09T19:41:31Z https://gatk.broadinstitute.org/hc/en-us/articles/21905097469723-CallCopyRatioSegments 2024-01-09T19:41:38Z https://gatk.broadinstitute.org/hc/en-us/articles/21905097719963-IlluminaLaneMetrics 2024-01-09T19:46:02Z https://gatk.broadinstitute.org/hc/en-us/articles/21905097788187-BamIndexStats-Picard 2024-01-09T19:46:03Z https://gatk.broadinstitute.org/hc/en-us/articles/21905098042907-TargetMetrics 2024-01-09T19:46:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21905098181403-VariantType 2024-01-09T19:41:46Z https://gatk.broadinstitute.org/hc/en-us/articles/21905098658843-TheoreticalSensitivityMetrics 2024-01-09T19:46:07Z https://gatk.broadinstitute.org/hc/en-us/articles/21905099884443-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2024-01-09T19:42:04Z https://gatk.broadinstitute.org/hc/en-us/articles/21905101474971-FlagStat 2024-01-09T19:46:22Z https://gatk.broadinstitute.org/hc/en-us/articles/21905101539739-CombineGenotypingArrayVcfs-Picard 2024-01-09T19:46:22Z https://gatk.broadinstitute.org/hc/en-us/articles/21905101644315-BaitDesigner-Picard 2024-01-09T19:46:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21905101848219-InbreedingCoeff 2024-01-09T19:42:22Z https://gatk.broadinstitute.org/hc/en-us/articles/21905102160795-PrintVariantsSpark 2024-01-09T19:46:26Z https://gatk.broadinstitute.org/hc/en-us/articles/21905102332059-FlowBasedTPAttributeValidReadFilter 2024-01-09T19:42:27Z https://gatk.broadinstitute.org/hc/en-us/articles/21905103407003-CollectRnaSeqMetrics-Picard 2024-01-09T19:42:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21905105244059-ReadPosition 2024-01-09T19:41:58Z https://gatk.broadinstitute.org/hc/en-us/articles/21905105450011-ReadStrandFilter 2024-01-09T19:42:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21905106064027-IndelLength 2024-01-09T19:42:08Z https://gatk.broadinstitute.org/hc/en-us/articles/21905106151963-ValidateVariants 2024-01-09T19:46:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905107026587-QualityScoreDistribution-Picard 2024-01-09T19:42:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905107468955-IlluminaPhasingMetrics 2024-01-09T19:46:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21905108121371-BpmToNormalizationManifestCsv-Picard 2024-01-09T19:46:27Z https://gatk.broadinstitute.org/hc/en-us/articles/21905109334043-GatherVcfsCloud-BETA 2024-01-09T19:42:40Z https://gatk.broadinstitute.org/hc/en-us/articles/21905109503131-PathSeqScoreSpark 2024-01-09T19:46:33Z https://gatk.broadinstitute.org/hc/en-us/articles/21905109781147-AS-MappingQualityRankSumTest 2024-01-09T19:42:45Z https://gatk.broadinstitute.org/hc/en-us/articles/21905109920923-BaseQuality 2024-01-09T19:42:47Z https://gatk.broadinstitute.org/hc/en-us/articles/21905109989275-SeqIsStoredReadFilter 2024-01-09T19:42:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21905110546075-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2024-01-09T19:46:41Z https://gatk.broadinstitute.org/hc/en-us/articles/21905110639259-SVConcordance-BETA 2024-01-09T19:46:41Z https://gatk.broadinstitute.org/hc/en-us/articles/21905110935835-CycleSkipStatus 2024-01-09T19:42:59Z https://gatk.broadinstitute.org/hc/en-us/articles/21905111522459-JointGermlineCNVSegmentation-BETA 2024-06-28T13:30:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21905111850267-ProperlyPairedReadFilter 2024-01-09T19:43:09Z https://gatk.broadinstitute.org/hc/en-us/articles/21905112242075-CrosscheckFingerprints-Picard 2024-01-09T19:46:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905113002139-Concordance 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905113856795-ValidateSamFile-Picard 2024-01-09T19:42:27Z https://gatk.broadinstitute.org/hc/en-us/articles/21905114313627-ReadGroupBlackListReadFilter 2024-01-09T19:42:31Z https://gatk.broadinstitute.org/hc/en-us/articles/21905114779675-CollectIlluminaBasecallingMetrics-Picard 2024-01-09T19:42:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21905115624603-SplitReads 2024-01-09T19:46:35Z https://gatk.broadinstitute.org/hc/en-us/articles/21905115981211-IntervalOverlapReadFilter 2024-01-09T19:42:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21905116134299-RampedHaplotypeCaller-EXPERIMENTAL 2024-01-09T19:46:37Z https://gatk.broadinstitute.org/hc/en-us/articles/21905116203419-GroundTruthReadsBuilder-EXPERIMENTAL 2024-01-09T19:46:38Z https://gatk.broadinstitute.org/hc/en-us/articles/21905116362779-VariantRecalibrator 2024-01-09T19:46:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21905117233563-EvaluateInfoFieldConcordance-BETA 2024-01-09T19:46:45Z https://gatk.broadinstitute.org/hc/en-us/articles/21905118107931-FilterFuncotations-EXPERIMENTAL 2024-01-09T19:46:49Z https://gatk.broadinstitute.org/hc/en-us/articles/21905118377755-GenotypeGVCFs 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905118456603-TandemRepeat 2024-01-09T19:43:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905118698779-AnalyzeSaturationMutagenesis-BETA 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905119092891-BuildBamIndex-Picard 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905120742555-CountNs 2024-01-09T19:43:40Z https://gatk.broadinstitute.org/hc/en-us/articles/21905120810267-InsertSizeMetrics 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905121125275-CollectOxoGMetrics-Picard 2024-05-13T15:21:16Z https://gatk.broadinstitute.org/hc/en-us/articles/21905121509403-CountBasesSpark 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905122450203-GcBiasDetailMetrics 2024-01-09T19:46:30Z https://gatk.broadinstitute.org/hc/en-us/articles/21905122797723-MergeSamFiles-Picard 2024-01-09T19:46:32Z https://gatk.broadinstitute.org/hc/en-us/articles/21905123042459-AnnotateIntervals 2024-01-09T19:46:33Z https://gatk.broadinstitute.org/hc/en-us/articles/21905123507611-ReadPosRankSumTest 2024-01-09T19:42:46Z https://gatk.broadinstitute.org/hc/en-us/articles/21905123962395-CollectBaseDistributionByCycleSpark-BETA 2024-01-09T19:46:38Z https://gatk.broadinstitute.org/hc/en-us/articles/21905124494619-SplitIntervals 2024-01-09T19:46:42Z https://gatk.broadinstitute.org/hc/en-us/articles/21905124739483-UnmarkDuplicates 2024-01-09T19:46:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21905125488027-BaseErrorMetric 2024-01-09T19:46:48Z https://gatk.broadinstitute.org/hc/en-us/articles/21905125788187-SplitVcfs-Picard 2024-01-09T19:46:49Z https://gatk.broadinstitute.org/hc/en-us/articles/21905126346523-FindBadGenomicKmersSpark-BETA 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905126590491-AS-QualByDepth 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905126659099-AS-BaseQualityRankSumTest 2024-01-09T19:43:21Z https://gatk.broadinstitute.org/hc/en-us/articles/21905127088027-NotSecondaryAlignmentReadFilter 2024-01-09T19:43:25Z https://gatk.broadinstitute.org/hc/en-us/articles/21905127851675-MetricsReadFilter 2024-01-09T19:43:31Z https://gatk.broadinstitute.org/hc/en-us/articles/21905128307227-DepthPerSampleHC 2024-01-09T19:43:36Z https://gatk.broadinstitute.org/hc/en-us/articles/21905128851355-ReadAnonymizer-EXPERIMENTAL 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905128929435-MappingQualityAvailableReadFilter 2024-01-09T19:43:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21905129540507-ASEReadCounter 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905129631259-CalibrateDragstrModel 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905130026267-HmerMotifs 2024-01-09T19:43:56Z https://gatk.broadinstitute.org/hc/en-us/articles/21905130408219-ConvertHeaderlessHadoopBamShardToBam-BETA 2024-01-09T19:42:37Z https://gatk.broadinstitute.org/hc/en-us/articles/21905131542939-NonZeroReferenceLengthAlignmentReadFilter 2024-01-09T19:42:49Z https://gatk.broadinstitute.org/hc/en-us/articles/21905132012955-PathSeqFilterSpark 2024-01-09T19:46:40Z https://gatk.broadinstitute.org/hc/en-us/articles/21905132400667-FastaAlternateReferenceMaker 2024-01-09T19:46:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21905133224859-DepthOfCoverage-BETA 2024-02-06T00:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/21905133311515-PileupSpark-BETA 2024-01-09T19:46:47Z https://gatk.broadinstitute.org/hc/en-us/articles/21905133881755-SplitSamByLibrary-Picard 2024-01-09T19:46:50Z https://gatk.broadinstitute.org/hc/en-us/articles/21905135035931-CollectRrbsMetrics-Picard 2024-01-09T19:43:25Z https://gatk.broadinstitute.org/hc/en-us/articles/21905135628571-IndexFeatureFile 2024-01-09T19:43:31Z https://gatk.broadinstitute.org/hc/en-us/articles/21905136080411-QualityScoreDistributionSpark-BETA 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905137669019-CreateSomaticPanelOfNormals-BETA 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905138065051-CheckTerminatorBlock-Picard 2024-01-09T19:43:57Z https://gatk.broadinstitute.org/hc/en-us/articles/21905138545307-IndependentReplicateMetric 2024-01-09T19:46:27Z https://gatk.broadinstitute.org/hc/en-us/articles/21905138642203-FastqToSam-Picard 2024-01-09T19:46:28Z https://gatk.broadinstitute.org/hc/en-us/articles/21905138865179-SamToFastq-Picard 2024-01-09T19:46:29Z https://gatk.broadinstitute.org/hc/en-us/articles/21905138975515-SortSam-Picard 2024-01-09T19:46:30Z https://gatk.broadinstitute.org/hc/en-us/articles/21905139249691-FuncotatorDataSourceDownloader 2024-01-09T19:42:36Z https://gatk.broadinstitute.org/hc/en-us/articles/21905139883291-RevertSam-Picard 2024-01-09T19:46:34Z https://gatk.broadinstitute.org/hc/en-us/articles/21905139950875-PassesVendorQualityCheckReadFilter 2024-01-09T19:42:43Z https://gatk.broadinstitute.org/hc/en-us/articles/21905141585307-StructuralVariationDiscoveryPipelineSpark-BETA 2024-01-09T19:46:44Z https://gatk.broadinstitute.org/hc/en-us/articles/21905141738267-SplitNCigarReads 2024-01-09T19:46:45Z https://gatk.broadinstitute.org/hc/en-us/articles/21905141804187-NonZeroFragmentLengthReadFilter 2024-01-09T19:43:05Z https://gatk.broadinstitute.org/hc/en-us/articles/21905142403995-CigarContainsNoNOperator 2024-01-09T19:43:10Z https://gatk.broadinstitute.org/hc/en-us/articles/21905142784923-CNNVariantTrain-EXPERIMENTAL 2024-06-25T07:11:20Z https://gatk.broadinstitute.org/hc/en-us/articles/21905143537307-FragmentLengthReadFilter 2024-01-09T19:43:23Z https://gatk.broadinstitute.org/hc/en-us/articles/21905143850395-FindMendelianViolations-Picard 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905143942555-WgsMetricsWithNonZeroCoverage 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905144018203-IndelErrorMetric 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905144089115-ShiftFasta-BETA 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905144369819-ValidAlignmentEndReadFilter 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905144573211-FastaReferenceMaker 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905145002907-OrientationBiasReadCounts 2024-01-09T19:43:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21905145287835-RenameSampleInVcf-Picard 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905145639835-CollectDuplicateMetrics-Picard 2024-01-09T19:43:47Z https://gatk.broadinstitute.org/hc/en-us/articles/21905145917723-PrintReadsSpark 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905146295707-FilterVariantTranches 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905146701595-QualityYieldMetrics 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905147210139-ReferenceBases 2024-01-09T19:43:30Z https://gatk.broadinstitute.org/hc/en-us/articles/21905147544603-FingerprintingDetailMetrics 2024-06-25T07:11:18Z https://gatk.broadinstitute.org/hc/en-us/articles/21905147896347-AlleleFraction 2024-01-09T19:43:37Z https://gatk.broadinstitute.org/hc/en-us/articles/21905148090139-AssemblyComplexity 2024-01-09T19:43:39Z https://gatk.broadinstitute.org/hc/en-us/articles/21905148610459-CreateReadCountPanelOfNormals 2024-01-09T19:43:46Z https://gatk.broadinstitute.org/hc/en-us/articles/21905148753947-CountReadsSpark 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/21905150024219-CleanSam-Picard 2024-01-09T19:43:59Z https://gatk.broadinstitute.org/hc/en-us/articles/21905155297435-PlotDenoisedCopyRatios 2024-01-09T19:42:57Z https://gatk.broadinstitute.org/hc/en-us/articles/21905155724827-HmerIndelNuc 2024-01-09T19:43:01Z https://gatk.broadinstitute.org/hc/en-us/articles/21905157536539-AddCommentsToBam-Picard 2024-06-25T07:11:19Z https://gatk.broadinstitute.org/hc/en-us/articles/21905159443739-ConvertSequencingArtifactToOxoG-Picard 2024-01-09T19:43:38Z https://gatk.broadinstitute.org/hc/en-us/articles/21905160936475-GtcToVcf-Picard 2024-01-09T19:43:55Z https://gatk.broadinstitute.org/hc/en-us/articles/21905161290267-ReadLengthReadFilter 2024-01-09T19:43:58Z https://gatk.broadinstitute.org/hc/en-us/articles/21905172369819-CheckPileup 2024-06-25T07:11:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007892530331-DumpTabixIndex 2024-06-30T00:48:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27007892566171-NonChimericOriginalAlignmentReadFilter 2024-06-30T00:48:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007892580379-MeanQualityByCycle-Picard 2024-06-30T00:53:02Z https://gatk.broadinstitute.org/hc/en-us/articles/27007892687387-OverclippedReadFilter 2024-06-30T00:48:39Z https://gatk.broadinstitute.org/hc/en-us/articles/27007892709403-BwaMemIndexImageCreator 2024-06-30T00:53:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007892831515-RMSMappingQuality 2024-06-30T00:48:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007892873755-Funcotator 2024-06-30T00:53:07Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893008411-VariantEval-BETA 2024-06-30T00:48:52Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893019547-GcBiasSummaryMetrics 2024-06-30T00:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893071003-CollectHsMetrics-Picard 2024-06-30T00:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893095579-AccumulateQualityYieldMetrics-Picard 2024-06-30T00:48:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893237403-ErrorMetric 2024-06-30T00:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893334043-BaseDistributionByCycleMetrics 2024-06-30T00:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893347611-OverlappingErrorMetric 2024-06-30T00:53:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893393179-PreAdapterSummaryMetrics 2024-06-30T00:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007893849371-AlleleFrequencyQCMetric 2024-06-30T00:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894000923-IlluminaBasecallsToFastq-Picard 2024-06-30T00:49:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894072603-FisherStrand 2024-06-30T00:49:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894326555-SetNmMdAndUqTags-Picard 2024-06-30T00:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894407835-BaitBiasSummaryMetrics 2024-06-30T00:53:36Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894419483-CalculateFingerprintMetrics-Picard 2024-06-30T00:49:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894501531-CollectAlignmentSummaryMetrics-Picard 2024-06-30T00:49:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894698267-CollectReadCounts 2024-06-30T00:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894793243-MappingQualityRankSumTest 2024-06-30T00:50:01Z https://gatk.broadinstitute.org/hc/en-us/articles/27007894860315-HaplotypeCallerSpark-BETA 2024-06-30T00:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27007895038107-FilterMutectCalls 2024-06-30T00:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007895061915-FingerprintMetrics 2024-06-30T00:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007895147291-CalculateMixingFractions 2024-06-30T00:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912356379-ExcessiveEndClippedReadFilter 2024-06-30T00:48:42Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912375451-BarcodeMetric 2024-06-30T00:53:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912413083-SampleReadFilter 2024-06-30T00:48:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912510747-PathSeqPipelineSpark 2024-06-30T00:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912525595-CalcMetadataSpark-BETA 2024-06-30T00:53:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912655131-CountReads 2024-06-30T00:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912713755-IlluminaBasecallingMetrics 2024-06-30T00:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912735771-GnarlyGenotyper-BETA 2024-06-30T00:53:12Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912771099-EstimateLibraryComplexity-Picard 2024-06-30T00:48:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912815131-ViewSam-Picard 2024-06-30T00:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912864411-CountVariants 2024-06-30T00:53:15Z https://gatk.broadinstitute.org/hc/en-us/articles/27007912999835-VariantAnnotator 2024-06-30T00:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913052315-BafRegressMetrics 2024-06-30T00:53:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913066139-CollectMultipleMetricsSpark-BETA 2024-06-30T00:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913089691-CompareReferences-EXPERIMENTAL 2024-06-30T00:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913112987-CountBases 2024-06-30T00:53:20Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913137691-StrandOddsRatio 2024-06-30T00:49:13Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913239067-HasReadGroupReadFilter 2024-06-30T00:49:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913319451-FlowFeatureMapper-EXPERIMENTAL 2024-06-30T00:53:24Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913421979-AS-RMSMappingQuality 2024-06-30T00:49:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913607835-ClusterCrosscheckMetrics-Picard 2024-06-30T00:49:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913634331-ClipReads 2024-06-30T00:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913728795-GetSampleName 2024-06-30T00:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913743771-CollectSVEvidence-BETA 2024-06-30T00:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913840027-GcBiasMetrics 2024-06-30T00:53:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913885083-FuncotateSegments-BETA 2024-06-30T00:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007913904923-GatherBamFiles-Picard 2024-06-30T00:49:41Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914026139-MappedReadFilter 2024-06-30T00:49:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914033819-ExtractSequences-Picard 2024-06-30T00:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914063387-MarkDuplicatesWithMateCigar-Picard 2024-06-30T00:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914069019-GatherBQSRReports 2024-06-30T00:49:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914097947-CpxVariantReInterpreterSpark-BETA 2024-06-30T00:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914112155-PathSeqBuildKmers 2024-06-30T00:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914130075-IntervalListTools-Picard 2024-06-30T00:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914209307-SortSamSpark-BETA 2024-06-30T00:53:44Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914345883-GetNormalArtifactData 2024-06-30T00:53:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914465051-ComposeSTRTableFile 2024-06-30T00:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914710299-AccumulateVariantCallingMetrics-Picard 2024-06-30T00:50:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914857627-GenomicsDBImport 2024-08-01T09:08:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27007914990491-PrintReads 2024-06-30T00:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915069211-MateDistantReadFilter 2024-06-30T00:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915444763-MeanQualityByCycleSpark-BETA 2024-06-30T00:54:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915472027-CheckIlluminaDirectory-Picard 2024-06-30T00:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915489307-CollectTargetedPcrMetrics-Picard 2024-06-30T00:54:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915523739-RrbsSummaryMetrics 2024-06-30T00:54:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915736987-AmbiguousBaseReadFilter 2024-06-30T00:50:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915773083-RemoveNearbyIndels 2024-06-30T00:54:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915812123-HmerIndelLength 2024-06-30T00:50:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915928475-AllelePseudoDepth 2024-06-30T00:50:53Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915970715-PositionBasedDownsampleSam-Picard 2024-06-30T00:50:55Z https://gatk.broadinstitute.org/hc/en-us/articles/27007915998107-PreAdapterDetailMetrics 2024-06-30T00:54:15Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916157979-PairedReadFilter 2024-06-30T00:51:02Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916224539-GetPileupSummaries 2024-06-30T00:54:21Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916333595-BaseRecalibrator 2024-06-30T00:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916446107-ClippingRankSumTest 2024-06-30T00:51:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916473499-CompareSAMs-Picard 2024-06-30T00:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916499355-BQSRPipelineSpark-BETA 2024-06-30T00:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916578843-IndelClassify 2024-06-30T00:51:13Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916777627-MappingQualityZero 2024-06-30T00:51:21Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916956699-AddOrReplaceReadGroups-Picard 2024-06-30T00:51:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007916989339-PlotModeledSegments 2024-06-30T00:51:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917029275-CombineGVCFs 2024-06-30T00:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917192603-CalculateGenotypePosteriors 2024-06-30T00:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917295387-CNNScoreVariants 2024-07-13T16:09:00Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917455131-InbreedingCoeff 2024-06-30T00:51:52Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917588379-WgsMetrics 2024-06-30T00:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917679771-ConvertHeaderlessHadoopBamShardToBam-BETA 2024-06-30T00:52:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917944987-VariantRecalibrator 2024-06-30T00:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/27007917991707-SVConcordance-BETA 2024-06-30T00:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918012827-SplitIntervals 2024-06-30T00:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918091035-UnmarkDuplicates 2024-06-30T00:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918102939-HmerIndelNuc 2024-06-30T00:52:20Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918112795-StructuralVariationDiscoveryPipelineSpark-BETA 2024-06-30T00:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918120731-EvaluateInfoFieldConcordance-BETA 2024-06-30T00:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918242715-ProperlyPairedReadFilter 2024-06-30T00:52:26Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918258459-CigarContainsNoNOperator 2024-06-30T00:52:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918269467-SplitVcfs-Picard 2024-06-30T00:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918282139-FilterFuncotations-EXPERIMENTAL 2024-06-30T00:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918418203-AnalyzeSaturationMutagenesis-BETA 2024-06-30T00:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918439195-AS-BaseQualityRankSumTest 2024-06-30T00:52:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918535963-WgsMetricsWithNonZeroCoverage 2024-06-30T00:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918558619-IndelErrorMetric 2024-06-30T00:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918594203-IndexFeatureFile 2024-06-30T00:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918669595-DepthPerSampleHC 2024-06-30T00:52:44Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918792731-CollectOxoGMetrics-Picard 2024-06-30T00:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918806555-CreateReadCountPanelOfNormals 2024-06-30T00:52:50Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918859803-CountBasesSpark 2024-06-30T00:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918873499-PrintReadsSpark 2024-06-30T00:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918966171-HmerMotifs 2024-06-30T00:52:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27007918974107-QualityYieldMetrics 2024-06-30T00:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/27007935362843-ChromosomeCounts 2024-06-30T00:48:32Z https://gatk.broadinstitute.org/hc/en-us/articles/27007935376411-LibraryReadFilter 2024-06-30T00:48:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007935517723-CollectHiSeqXPfFailMetrics-Picard 2024-06-30T00:48:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007935566107-GenotypeConcordance-Picard 2024-06-30T00:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007935696155-VerifyIDIntensityContaminationMetrics 2024-06-30T00:53:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007936474139-FixVcfHeader-Picard 2024-06-30T00:53:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007936993051-NotDuplicateReadFilter 2024-06-30T00:49:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007937127707-VariantCallingSummaryMetrics 2024-06-30T00:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007942374299-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2024-06-30T00:48:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27007942683931-NotProperlyPairedReadFilter 2024-06-30T00:48:41Z https://gatk.broadinstitute.org/hc/en-us/articles/27007942818331-AnalyzeCovariates 2024-06-30T00:53:06Z https://gatk.broadinstitute.org/hc/en-us/articles/27007942868507-FirstOfPairReadFilter 2024-06-30T00:48:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007943045787-SecondOfPairReadFilter 2024-06-30T00:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007943453979-JumpingLibraryMetrics 2024-06-30T00:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/27007943601691-LiftOverIntervalList-Picard 2024-06-30T00:49:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007943662107-BamToBfq-Picard 2024-06-30T00:49:06Z https://gatk.broadinstitute.org/hc/en-us/articles/27007943787419-FilterSamReads-Picard 2024-06-30T00:53:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944031643--Tool-Documentation-Index 2024-06-30T00:53:21Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944129691-DetermineGermlineContigPloidy 2024-06-30T00:49:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944144795-FindBreakpointEvidenceSpark-BETA 2024-06-30T00:53:23Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944235547-QualByDepth 2024-06-30T00:49:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944415515-NormalizeFasta-Picard 2024-06-30T00:53:26Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944492699-PFFailSummaryMetric 2024-06-30T00:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944556187-UpdateVCFSequenceDictionary 2024-06-30T00:53:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944616987-SamFormatConverter-Picard 2024-06-30T00:49:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944645403-PostProcessReadsForRSEM-BETA 2024-06-30T00:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944714651-GeneExpressionEvaluation-BETA 2024-06-30T00:53:29Z https://gatk.broadinstitute.org/hc/en-us/articles/27007944949659-SiteDepthtoBAF-EXPERIMENTAL 2024-06-30T00:53:32Z https://gatk.broadinstitute.org/hc/en-us/articles/27007945004059-CalculateReadGroupChecksum-Picard 2024-06-30T00:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007945230875-PathSeqBuildReferenceTaxonomy 2024-06-30T00:49:44Z https://gatk.broadinstitute.org/hc/en-us/articles/27007945249819-AS-FisherStrand 2024-06-30T00:49:44Z https://gatk.broadinstitute.org/hc/en-us/articles/27007945419419-GenotypeConcordanceContingencyMetrics 2024-06-30T00:53:39Z https://gatk.broadinstitute.org/hc/en-us/articles/27007950160795-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2024-06-30T00:53:00Z https://gatk.broadinstitute.org/hc/en-us/articles/27007950952475-AlignmentAgreesWithHeaderReadFilter 2024-06-30T00:48:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007951021851-FilterVcf-Picard 2024-06-30T00:48:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007951740187-MergePedIntoVcf-Picard 2024-06-30T00:49:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007951768603-PrimaryLineReadFilter 2024-06-30T00:49:10Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952084635-UniqueAltReadCount 2024-06-30T00:49:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952115739-MappingQuality 2024-06-30T00:49:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952230043-VariantsToTable 2024-06-30T00:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952273435-AddFlowSNVQuality-EXPERIMENTAL 2024-06-30T00:53:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952421787-CNNVariantWriteTensors-EXPERIMENTAL 2024-06-30T00:53:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952743707-PSFilterMetrics 2024-06-30T00:53:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952777243-ReadGroupHasFlowOrderReadFilter 2024-06-30T00:49:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007952904475-DepthPerAlleleBySample 2024-06-30T00:49:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007953023899-CompareMetrics-Picard 2024-06-30T00:53:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007953200155-CompareBaseQualities 2024-06-30T00:49:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007953219099-BwaSpark-BETA 2024-06-30T00:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007953333275-CollectSequencingArtifactMetrics-Picard 2024-06-30T00:49:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007953372443-GatherVcfs-Picard 2024-06-30T00:49:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007953758619-FragmentDepthPerAlleleBySample 2024-06-30T00:49:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27007953918363-FilterIntervals 2024-06-30T00:50:00Z https://gatk.broadinstitute.org/hc/en-us/articles/27007956829083-Pileup 2024-06-30T00:53:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007957070875-WellformedReadFilter 2024-06-30T00:53:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27007957288091-CollectQualityYieldMetrics-Picard 2024-06-30T00:48:47Z https://gatk.broadinstitute.org/hc/en-us/articles/27007957444251-AS-StrandOddsRatio 2024-06-30T00:48:50Z https://gatk.broadinstitute.org/hc/en-us/articles/27007957511323-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2024-06-30T00:53:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007957597723-RnaSeqMetrics 2024-06-30T00:53:10Z https://gatk.broadinstitute.org/hc/en-us/articles/27007957944475-PrintReadsHeader 2024-06-30T00:53:13Z https://gatk.broadinstitute.org/hc/en-us/articles/27007958018459-AnnotateVcfWithExpectedAlleleFraction 2024-06-30T00:53:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007958129051-AllowAllReadsReadFilter 2024-06-30T00:49:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007958397211-ArraysControlCodesSummaryMetrics 2024-06-30T00:53:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007958811547-MendelianViolationMetrics 2024-06-30T00:53:22Z https://gatk.broadinstitute.org/hc/en-us/articles/27007958832667-CheckFingerprint-Picard 2024-06-30T00:49:15Z https://gatk.broadinstitute.org/hc/en-us/articles/27007959165211-HaplotypeBasedVariantRecaller-EXPERIMENTAL 2024-06-30T00:53:26Z https://gatk.broadinstitute.org/hc/en-us/articles/27007959918363-MarkDuplicatesSpark 2024-06-30T00:53:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007959984539-HaplotypeFilteringAnnotation 2024-06-30T00:49:38Z https://gatk.broadinstitute.org/hc/en-us/articles/27007960425883-AnnotateVcfWithBamDepth 2024-06-30T00:53:38Z https://gatk.broadinstitute.org/hc/en-us/articles/27007961474459-MateDifferentStrandReadFilter 2024-06-30T00:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962371099-SVCluster-BETA 2024-06-30T00:53:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962440475-MappingQualityReadFilter 2024-06-30T00:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962491547-CollectQualityYieldMetricsSpark-BETA 2024-06-30T00:53:53Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962516507-FlowPairHMMAlignReadsToHaplotypes-EXPERIMENTAL 2024-06-30T00:53:54Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962569499-RawGtCount 2024-06-30T00:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962657051-HmerQualitySymetricReadFilter 2024-06-30T00:50:21Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962676507-BwaAndMarkDuplicatesPipelineSpark-BETA 2024-06-30T00:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962724507-HaplotypeCaller 2024-06-30T00:53:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007962939163-ClusteredCrosscheckMetric 2024-06-30T00:54:00Z https://gatk.broadinstitute.org/hc/en-us/articles/27007963002267-PathSeqBwaSpark 2024-06-30T00:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/27007963355675-ModelSegments 2024-06-30T00:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/27007963395227-RevertSamSpark-BETA 2024-06-30T00:54:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27007963435291-PFFailDetailedMetric 2024-06-30T00:54:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007963927451-AS-ReadPosRankSumTest 2024-06-30T00:51:02Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964085787-GatherTranches-BETA 2024-06-30T00:51:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964299547-PossibleDeNovo 2024-06-30T00:51:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964375451-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2024-06-30T00:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964420635-GermlineCNVCaller 2024-06-30T00:51:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964584219-CollectArraysVariantCallingMetrics-Picard 2024-06-30T00:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964598811-TargetMetrics 2024-06-30T00:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964610331-SVAnnotate 2024-06-30T00:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964741147-QualityYieldMetricsFlow 2024-06-30T00:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964749467-CollectGcBiasMetrics-Picard 2024-06-30T00:51:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964764955-ArraysVariantCallingSummaryMetrics 2024-06-30T00:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964819483-ReadStrandFilter 2024-06-30T00:51:39Z https://gatk.broadinstitute.org/hc/en-us/articles/27007964878363-MergeVcfs-Picard 2024-06-30T00:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965045787-MethylationTypeCaller-EXPERIMENTAL 2024-06-30T00:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965146907-CombineGenotypingArrayVcfs-Picard 2024-06-30T00:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965167387-BaitDesigner-Picard 2024-06-30T00:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965261211-IndependentReplicateMetric 2024-06-30T00:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965338267-SortSam-Picard 2024-06-30T00:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965347483-GcBiasDetailMetrics 2024-06-30T00:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965481371-AnnotateIntervals 2024-06-30T00:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965506715-PathSeqScoreSpark 2024-06-30T00:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965523483-RevertSam-Picard 2024-06-30T00:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965611931-SeqIsStoredReadFilter 2024-06-30T00:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965621275-IntervalOverlapReadFilter 2024-06-30T00:52:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965660187-GroundTruthReadsBuilder-EXPERIMENTAL 2024-06-30T00:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/27007965771931-FastaAlternateReferenceMaker 2024-06-30T00:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966050843-SplitSamByLibrary-Picard 2024-06-30T00:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966111899-TandemRepeat 2024-06-30T00:52:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966255131-BuildBamIndex-Picard 2024-06-30T00:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966273051-CollectRrbsMetrics-Picard 2024-06-30T00:52:36Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966363291-ShiftFasta-BETA 2024-06-30T00:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966414491-MetricsReadFilter 2024-06-30T00:52:41Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966461083-FastaReferenceMaker 2024-06-30T00:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966505499-AlleleFraction 2024-06-30T00:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966609435-ReadAnonymizer-EXPERIMENTAL 2024-06-30T00:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27007966668187-CollectDuplicateMetrics-Picard 2024-06-30T00:52:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007971422363-FlowBasedTPAttributeSymetricReadFilter 2024-06-30T00:49:21Z https://gatk.broadinstitute.org/hc/en-us/articles/27007971693979-CountVariantsSpark 2024-06-30T00:49:26Z https://gatk.broadinstitute.org/hc/en-us/articles/27007972048923-CollectSamErrorMetrics-Picard 2024-06-30T00:49:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007972105115-SoftClippedReadFilter 2024-06-30T00:49:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27007972690331-SamComparisonMetric 2024-06-30T00:53:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007973095963-ApplyBQSR 2024-06-30T00:53:41Z https://gatk.broadinstitute.org/hc/en-us/articles/27007973801243-SplitSamByNumberOfReads-Picard 2024-06-30T00:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/27007974096667-BaseRecalibratorSpark-BETA 2024-06-30T00:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007975223579-ReadsPipelineSpark-BETA 2024-06-30T00:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/27007975368859-CollectIlluminaLaneMetrics-Picard 2024-06-30T00:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007975458715-JexlExpressionReadTagValueFilter 2024-06-30T00:50:29Z https://gatk.broadinstitute.org/hc/en-us/articles/27007975650075-SampleList 2024-06-30T00:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007975860507-CollectBaseDistributionByCycle-Picard 2024-06-30T00:50:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007975911835-RrbsCpgDetailMetrics 2024-06-30T00:54:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27007976065819-ExtractIlluminaBarcodes-Picard 2024-06-30T00:50:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27007976313243-GcContent 2024-06-30T00:50:50Z https://gatk.broadinstitute.org/hc/en-us/articles/27007976361883-VcfToAdpc-Picard 2024-06-30T00:50:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007976516507-CheckReferenceCompatibility-EXPERIMENTAL 2024-06-30T00:54:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007976575899-RawWgsMetrics 2024-06-30T00:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27007976623003-PSScoreMetrics 2024-06-30T00:54:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007976745627-UmiMetrics 2024-06-30T00:54:20Z https://gatk.broadinstitute.org/hc/en-us/articles/27007977045275-GenotypeConcordanceDetailMetrics 2024-06-30T00:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007977567387-DenoiseReadCounts 2024-06-30T00:51:15Z https://gatk.broadinstitute.org/hc/en-us/articles/27007977971227-CollectQualityYieldMetricsSNVQ-Picard 2024-06-30T00:51:23Z https://gatk.broadinstitute.org/hc/en-us/articles/27007978347163-CollectVariantCallingMetrics-Picard 2024-06-30T00:51:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007978536219-LiftoverVcf-Picard 2024-06-30T00:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/27007978620059-ReadPosition 2024-06-30T00:51:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007978655259-Coverage 2024-06-30T00:51:38Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979005083-CpcgMetrics 2024-06-30T00:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979072027-FingerprintingSummaryMetrics 2024-06-30T00:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979091611-PreprocessIntervals 2024-06-30T00:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979130395-CalculateContamination 2024-06-30T00:53:40Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979261595-MakeSitesOnlyVcf-Picard 2024-06-30T00:53:42Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979318811-CollectInsertSizeMetrics-Picard 2024-06-30T00:49:55Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979341723-StrandBiasBySample 2024-06-30T00:49:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979381915-LearnReadOrientationModel 2024-06-30T00:49:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979480987-LeftAlignIndels 2024-06-30T00:53:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979726491-CollectJumpingLibraryMetrics-Picard 2024-06-30T00:50:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007979856027-NonNFastaSize-Picard 2024-06-30T00:53:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980034075-BaitBiasDetailMetrics 2024-06-30T00:53:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980088987-SelectVariants 2024-06-30T00:53:50Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980150811-IlluminaBasecallsToSam-Picard 2024-06-30T00:50:12Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980568603-GenotypeConcordanceSummaryMetrics 2024-06-30T00:53:55Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980736155-AlignmentSummaryMetrics 2024-06-30T00:53:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980831131-ReplaceSamHeader-Picard 2024-06-30T00:53:58Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980899483-MateUnmappedAndUnmappedReadFilter 2024-06-30T00:50:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007980992667-CountBasesInReference 2024-06-30T00:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27007981068187-VcfToIntervalList-Picard 2024-06-30T00:54:00Z https://gatk.broadinstitute.org/hc/en-us/articles/27007981110555-SetNmAndUqTags-Picard 2024-06-30T00:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/27007981263771-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2024-06-30T00:54:02Z https://gatk.broadinstitute.org/hc/en-us/articles/27007981529243-TrainVariantAnnotationsModel-BETA 2024-06-30T00:54:06Z https://gatk.broadinstitute.org/hc/en-us/articles/27007981559835-MergeBamAlignment-Picard 2024-06-30T00:50:40Z https://gatk.broadinstitute.org/hc/en-us/articles/27007981883163-CompareDuplicatesSpark-BETA 2024-06-30T00:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/27007982580763-FlagStatSpark 2024-06-30T00:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007982609435-FilterAlignmentArtifacts-EXPERIMENTAL 2024-06-30T00:54:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007982805275-FifoBuffer-Picard 2024-06-30T00:51:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007982861595-VariantFiltration 2024-06-30T00:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27007982944411-RevertBaseQualityScores 2024-06-30T00:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983082651-VariantCallingDetailMetrics 2024-06-30T00:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983249179-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2024-06-30T00:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983280411-ArraysVariantCallingDetailMetrics 2024-06-30T00:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983426843-GroundTruthScorer-EXPERIMENTAL 2024-06-30T00:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983619611-ApplyVQSR 2024-06-30T00:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983722523-ExtractVariantAnnotations-BETA 2024-06-30T00:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983792283-CallCopyRatioSegments 2024-06-30T00:51:22Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983821211-ScatterIntervalsByNs-Picard 2024-06-30T00:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/27007983962651-IlluminaLaneMetrics 2024-06-30T00:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984138011-VariantType 2024-06-30T00:51:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984158747-VcfFormatConverter-Picard 2024-06-30T00:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984740379-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2024-06-30T00:51:40Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984818075-WellformedFlowBasedReadFilter 2024-06-30T00:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984831899-IndelLength 2024-06-30T00:51:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984884507-ValidateVariants 2024-08-17T04:35:39Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984926107-ExtractSVEvidenceSpark-BETA 2024-06-30T00:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27007984957595-CollectAllelicCounts 2024-06-30T00:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/27007985015835-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2024-06-30T00:51:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27007985321755-IlluminaPhasingMetrics 2024-06-30T00:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/27007985406747-FixMateInformation-Picard 2024-06-30T00:51:54Z https://gatk.broadinstitute.org/hc/en-us/articles/27007985477659-PrintVariantsSpark 2024-06-30T00:55:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007985659675-FastqToSam-Picard 2024-06-30T00:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/27007985839515-CollectIlluminaBasecallingMetrics-Picard 2024-06-30T00:52:02Z https://gatk.broadinstitute.org/hc/en-us/articles/27007986185115-SplitReads 2024-06-30T00:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27007986228251-ReadPosRankSumTest 2024-06-30T00:52:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007986356251-NonZeroReferenceLengthAlignmentReadFilter 2024-06-30T00:52:12Z https://gatk.broadinstitute.org/hc/en-us/articles/27007987147675-GenotypeGVCFs 2024-06-30T00:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007987543963-MappingQualityNotZeroReadFilter 2024-06-30T00:50:01Z https://gatk.broadinstitute.org/hc/en-us/articles/27007987722139-HsMetrics 2024-06-30T00:53:47Z https://gatk.broadinstitute.org/hc/en-us/articles/27007988136987-ScoreVariantAnnotations-BETA 2024-06-30T00:53:52Z https://gatk.broadinstitute.org/hc/en-us/articles/27007988195739-ReadGroupReadFilter 2024-06-30T00:50:14Z https://gatk.broadinstitute.org/hc/en-us/articles/27007988341019-PlatformUnitReadFilter 2024-06-30T00:50:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27007988409499-CreateBafRegressMetricsFile-Picard 2024-06-30T00:50:18Z https://gatk.broadinstitute.org/hc/en-us/articles/27007988482843-CreateHadoopBamSplittingIndex-BETA 2024-06-30T00:50:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27007988734491-ValidAlignmentStartReadFilter 2024-06-30T00:53:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27007988843931-CountFalsePositives-BETA 2024-06-30T00:53:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27007989676443-DuplicationMetrics 2024-06-30T00:54:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27007989945115-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2024-06-30T00:54:11Z https://gatk.broadinstitute.org/hc/en-us/articles/27007989978267-OriginalAlignment 2024-06-30T00:50:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990006555-MarkDuplicates-Picard 2024-06-30T00:50:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990059931-CreateSequenceDictionary-Picard 2024-07-27T23:02:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990132123-GoodCigarReadFilter 2024-06-30T00:50:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990161435-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2024-06-30T00:50:52Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990236827-TransmittedSingleton 2024-06-30T00:50:54Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990399131-ReorderSam-Picard 2024-06-30T00:50:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990480283-NotSupplementaryAlignmentReadFilter 2024-06-30T00:50:58Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990552475-GenotypeSummaries 2024-06-30T00:50:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990659739-CollectWgsMetrics-Picard 2024-06-30T00:51:01Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990867611-ExcessHet 2024-06-30T00:51:04Z https://gatk.broadinstitute.org/hc/en-us/articles/27007990924443-LikelihoodRankSumTest 2024-06-30T00:51:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27007991053723-DownsampleSam-Picard 2024-06-30T00:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007991590427-IntervalListToBed-Picard 2024-06-30T00:51:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27007991884571-PlatformReadFilter 2024-06-30T00:51:24Z https://gatk.broadinstitute.org/hc/en-us/articles/27007991962907-Mutect2 2024-06-30T00:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27007992217371-TheoreticalSensitivityMetrics 2024-06-30T00:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27007992264091-LocalAssembler-BETA 2024-06-30T00:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/27007992444699-AddOATag-Picard 2024-06-30T00:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/27007992617499-ApplyBQSRSpark-BETA 2024-06-30T00:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007993043995-QualityScoreDistribution-Picard 2024-06-30T00:51:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27007993307419-SortVcf-Picard 2024-06-30T00:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007993691163-FuncotatorDataSourceDownloader 2024-06-30T00:52:03Z https://gatk.broadinstitute.org/hc/en-us/articles/27007994313243-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2024-06-30T00:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27007994635547-SplitNCigarReads 2024-06-30T00:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/27007994657179-NonZeroFragmentLengthReadFilter 2024-06-30T00:52:23Z https://gatk.broadinstitute.org/hc/en-us/articles/27007994734235-PileupSpark-BETA 2024-06-30T00:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27007995049755-FindBadGenomicKmersSpark-BETA 2024-06-30T00:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27007995176731-Concordance 2024-06-30T00:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007995200539-FragmentLengthReadFilter 2024-06-30T00:52:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007995478939-FingerprintingDetailMetrics 2024-06-30T00:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27007995586843-OrientationBiasReadCounts 2024-06-30T00:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27007995696539-RenameSampleInVcf-Picard 2024-06-30T00:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007996715803-MarkIlluminaAdapters-Picard 2024-06-30T00:54:01Z https://gatk.broadinstitute.org/hc/en-us/articles/27007996784795-MatchingBasesAndQualsReadFilter 2024-06-30T00:50:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27007996896283-FragmentLength 2024-06-30T00:50:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007997020955-ReblockGVCF 2024-06-30T00:54:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27007997061275-FixMisencodedBaseQualityReads 2024-06-30T00:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/27007997088667-LeftAlignAndTrimVariants 2024-06-30T00:54:07Z https://gatk.broadinstitute.org/hc/en-us/articles/27007997206171-BedToIntervalList-Picard 2024-06-30T00:54:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27007997278875-CollectRawWgsMetrics-Picard 2024-06-30T00:54:10Z https://gatk.broadinstitute.org/hc/en-us/articles/27007997751707-PostprocessGermlineCNVCalls 2024-06-30T00:54:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27007998500891-TransferReadTags-EXPERIMENTAL 2024-06-30T00:54:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27007998606107-CollectInsertSizeMetricsSpark-BETA 2024-06-30T00:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007998700955-BaseQualityRankSumTest 2024-06-30T00:51:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27007998877083-UpdateVcfSequenceDictionary-Picard 2024-06-30T00:51:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27007998901787-ReadNameReadFilter 2024-06-30T00:51:20Z https://gatk.broadinstitute.org/hc/en-us/articles/27007998978715-ErrorSummaryMetrics 2024-06-30T00:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27007999062299-AS-InbreedingCoeff 2024-06-30T00:51:24Z https://gatk.broadinstitute.org/hc/en-us/articles/27007999140635-BamIndexStats-Picard 2024-06-30T00:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27007999511323-PrintReadCounts-EXPERIMENTAL 2024-06-30T00:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/27007999632539-ReadTagValueFilter 2024-06-30T00:51:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27007999670555-MateOnSameContigOrNoMappedMateReadFilter 2024-06-30T00:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/27007999730587-TargetedPcrMetrics 2024-06-30T00:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27007999833883-CollectMultipleMetrics-Picard 2024-06-30T00:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000157979-PrintDistantMates 2024-06-30T00:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000193947-FlagStat 2024-06-30T00:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000490139-ValidateSamFile-Picard 2024-06-30T00:51:55Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000550171-BpmToNormalizationManifestCsv-Picard 2024-06-30T00:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000624283-ReadGroupBlackListReadFilter 2024-06-30T00:51:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000667291-SamToFastq-Picard 2024-06-30T00:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000883099-MergeSamFiles-Picard 2024-06-30T00:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/27008000953627-GatherVcfsCloud 2024-06-30T00:52:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27008001144859-AS-MappingQualityRankSumTest 2024-06-30T00:52:09Z https://gatk.broadinstitute.org/hc/en-us/articles/27008001308827-RampedHaplotypeCaller-EXPERIMENTAL 2024-06-30T00:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/27008001574043-CycleSkipStatus 2024-06-30T00:52:19Z https://gatk.broadinstitute.org/hc/en-us/articles/27008001803931-JointGermlineCNVSegmentation-BETA 2024-06-30T00:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/27008001836187-DepthOfCoverage-BETA 2024-06-30T00:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/27008002243611-AddCommentsToBam-Picard 2024-06-30T00:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/27008002401307-NotSecondaryAlignmentReadFilter 2024-06-30T00:52:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27008002419611-FindMendelianViolations-Picard 2024-06-30T00:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/27008002921371-InsertSizeMetrics 2024-06-30T00:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27008003414299-CheckPileup 2024-06-30T00:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/27008003431195-GtcToVcf-Picard 2024-06-30T00:52:57Z https://gatk.broadinstitute.org/hc/en-us/articles/27008003479963-CheckTerminatorBlock-Picard 2024-06-30T00:52:58Z https://gatk.broadinstitute.org/hc/en-us/articles/27008003532187-CleanSam-Picard 2024-06-30T00:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27008012913563-ReadLengthEqualsCigarLengthReadFilter 2024-06-30T00:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27008013071899-FlowBasedTPAttributeValidReadFilter 2024-06-30T00:51:56Z https://gatk.broadinstitute.org/hc/en-us/articles/27008013441179-CollectRnaSeqMetrics-Picard 2024-06-30T00:52:05Z https://gatk.broadinstitute.org/hc/en-us/articles/27008013611419-PassesVendorQualityCheckReadFilter 2024-06-30T00:52:08Z https://gatk.broadinstitute.org/hc/en-us/articles/27008013766683-BaseQuality 2024-06-30T00:52:10Z https://gatk.broadinstitute.org/hc/en-us/articles/27008013925019-CollectBaseDistributionByCycleSpark-BETA 2024-06-30T00:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/27008013972379-PathSeqFilterSpark 2024-06-30T00:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/27008014046875-PlotDenoisedCopyRatios 2024-06-30T00:52:17Z https://gatk.broadinstitute.org/hc/en-us/articles/27008014441371-BaseErrorMetric 2024-06-30T00:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/27008014624667-CrosscheckFingerprints-Picard 2024-06-30T00:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/27008014645915-CNNVariantTrain-EXPERIMENTAL 2024-06-30T00:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/27008014783515-AS-QualByDepth 2024-06-30T00:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/27008015059483-ReferenceBases 2024-06-30T00:52:40Z https://gatk.broadinstitute.org/hc/en-us/articles/27008015129243-ValidAlignmentEndReadFilter 2024-06-30T00:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/27008015279003-ConvertSequencingArtifactToOxoG-Picard 2024-06-30T00:52:45Z https://gatk.broadinstitute.org/hc/en-us/articles/27008015365659-AssemblyComplexity 2024-06-30T00:52:46Z https://gatk.broadinstitute.org/hc/en-us/articles/27008015876379-FilterVariantTranches 2024-06-30T00:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27008015908379-CreateSomaticPanelOfNormals-BETA 2024-06-30T00:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/27008016030363-ReadLengthReadFilter 2024-06-30T00:52:59Z https://gatk.broadinstitute.org/hc/en-us/articles/27008021201179-QualityScoreDistributionSpark-BETA 2024-06-30T00:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/27008021336859-CountNs 2024-06-30T00:52:47Z https://gatk.broadinstitute.org/hc/en-us/articles/27008021453979-MappingQualityAvailableReadFilter 2024-06-30T00:52:49Z https://gatk.broadinstitute.org/hc/en-us/articles/27008021552027-CountReadsSpark 2024-06-30T00:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/27008021650331-ASEReadCounter 2024-06-30T00:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/27008029541787-CalibrateDragstrModel 2024-06-30T00:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30331956489499-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2024-10-24T01:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30331956579739-DumpTabixIndex 2024-10-24T01:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/30331970778907-CollectHiSeqXPfFailMetrics-Picard 2024-10-24T01:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30331970844443-OverclippedReadFilter 2024-10-24T01:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971128347-FilterVcf-Picard 2024-10-24T01:54:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971298459-CollectHsMetrics-Picard 2024-10-24T01:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971418395-PrintReadsHeader 2024-10-24T01:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971478939-AnnotateVcfWithExpectedAlleleFraction 2024-10-24T01:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971541659-LiftOverIntervalList-Picard 2024-10-24T01:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971637403-PreAdapterSummaryMetrics 2024-10-24T01:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971691035-VariantAnnotator 2024-10-24T01:54:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971797275-CollectMultipleMetricsSpark-BETA 2024-10-24T01:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971913371-CheckFingerprint-Picard 2024-10-24T01:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/30331971981851-UniqueAltReadCount 2024-10-24T01:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972014747-QualByDepth 2024-10-24T01:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972091675-AlleleFrequencyQCMetric 2024-10-24T01:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972114203-AddFlowSNVQuality-EXPERIMENTAL 2024-10-24T01:54:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972384667-PSFilterMetrics 2024-10-24T01:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972432411-SoftClippedReadFilter 2024-10-24T01:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972496795-MarkDuplicatesSpark 2024-10-24T01:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972790555-PathSeqBuildReferenceTaxonomy 2024-10-24T01:55:00Z https://gatk.broadinstitute.org/hc/en-us/articles/30331972855451-BwaSpark-BETA 2024-10-24T01:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/30331973157019-MarkDuplicatesWithMateCigar-Picard 2024-10-24T01:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/30331973217435-ApplyBQSR 2024-10-24T01:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/30331973267995-PathSeqBuildKmers 2024-10-24T01:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/30331973321499-IntervalListTools-Picard 2024-10-24T01:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/30331973394331-LearnReadOrientationModel 2024-10-24T01:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30331987823003-ChromosomeCounts 2024-10-24T01:54:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30331987860763-LibraryReadFilter 2024-10-24T01:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/30331988124187-ExcessiveEndClippedReadFilter 2024-10-24T01:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30331988165019-WellformedReadFilter 2024-10-24T01:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30331988329115-PathSeqPipelineSpark 2024-10-24T01:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/30331988400923-AlignmentAgreesWithHeaderReadFilter 2024-10-24T01:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30331988460059-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2024-10-24T01:54:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30331988657435-IlluminaBasecallingMetrics 2024-10-24T01:54:35Z https://gatk.broadinstitute.org/hc/en-us/articles/30331988744347-ViewSam-Picard 2024-10-24T01:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989184539-StrandOddsRatio 2024-10-24T01:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989211419--Tool-Documentation-Index 2024-10-24T01:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989262491-HasReadGroupReadFilter 2024-10-24T01:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989517723-AS-RMSMappingQuality 2024-10-24T01:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989581083-IlluminaBasecallsToFastq-Picard 2024-10-24T01:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989600923-SamFormatConverter-Picard 2024-10-24T01:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989697435-CollectSamErrorMetrics-Picard 2024-10-24T01:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989807515-SiteDepthtoBAF-EXPERIMENTAL 2024-10-24T01:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989882139-CalculateReadGroupChecksum-Picard 2024-10-24T01:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989955099-GcBiasMetrics 2024-10-24T01:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/30331989974043-CompareMetrics-Picard 2024-10-24T01:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/30331990150299-SamComparisonMetric 2024-10-24T01:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/30331997998619-Pileup 2024-10-24T01:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/30331998118171-BarcodeMetric 2024-10-24T01:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30331998491675-GcBiasSummaryMetrics 2024-10-24T01:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30331998566427-FixVcfHeader-Picard 2024-10-24T01:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003003035-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2024-10-24T01:54:23Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003182491-BwaMemIndexImageCreator 2024-10-24T01:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003197211-VerifyIDIntensityContaminationMetrics 2024-10-24T01:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003333787-AnalyzeCovariates 2024-10-24T01:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003370267-RMSMappingQuality 2024-10-24T01:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003399323-FirstOfPairReadFilter 2024-10-24T01:54:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003469595-CalcMetadataSpark-BETA 2024-10-24T01:54:30Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003486747-SecondOfPairReadFilter 2024-10-24T01:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30332003911451-CountVariants 2024-10-24T01:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/30332004138139-FilterSamReads-Picard 2024-10-24T01:54:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30332004542491-HaplotypeBasedVariantRecaller-EXPERIMENTAL 2024-10-24T01:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332004603803-CountVariantsSpark 2024-10-24T01:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332004699931-FisherStrand 2024-10-24T01:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005077019-FuncotateSegments-BETA 2024-10-24T01:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005176219-AS-FisherStrand 2024-10-24T01:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005197211-CompareBaseQualities 2024-10-24T01:55:01Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005338139-CollectSequencingArtifactMetrics-Picard 2024-10-24T01:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005382555-GatherVcfs-Picard 2024-10-24T01:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005529627-CpxVariantReInterpreterSpark-BETA 2024-10-24T01:55:06Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005573275-MakeSitesOnlyVcf-Picard 2024-10-24T01:55:07Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005631899-CollectInsertSizeMetrics-Picard 2024-10-24T01:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005669403-FragmentDepthPerAlleleBySample 2024-10-24T01:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30332005752347-LeftAlignIndels 2024-10-24T01:55:10Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006017947-BaseRecalibratorSpark-BETA 2024-10-24T01:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006054811-CalculateMixingFractions 2024-10-24T01:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006170139-ReadGroupReadFilter 2024-10-24T01:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006200603-GenomicsDBImport 2024-10-24T01:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006220315-PlatformUnitReadFilter 2024-10-24T01:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006231579-FlowPairHMMAlignReadsToHaplotypes-EXPERIMENTAL 2024-10-24T01:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006280603-RawGtCount 2024-10-24T01:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006386459-HaplotypeCaller 2024-10-24T01:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006617755-PathSeqBwaSpark 2024-10-24T01:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006655643-SampleList 2024-10-24T01:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006694811-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2024-10-24T01:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006847131-RrbsSummaryMetrics 2024-10-24T01:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332006945307-LeftAlignAndTrimVariants 2024-10-24T01:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007040411-GenotypeConcordance-Picard 2024-10-24T01:54:25Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007204379-SampleReadFilter 2024-10-24T01:54:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007363355-AS-StrandOddsRatio 2024-10-24T01:54:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007461275-RnaSeqMetrics 2024-10-24T01:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007482139-CountReads 2024-10-24T01:54:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007551131-AccumulateQualityYieldMetrics-Picard 2024-10-24T01:54:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007733531-ErrorMetric 2024-10-24T01:54:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007776283-AllowAllReadsReadFilter 2024-10-24T01:54:38Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007882267-VariantCallingSummaryMetrics 2024-10-24T01:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332007924763-ArraysControlCodesSummaryMetrics 2024-10-24T01:54:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008026011-PrimaryLineReadFilter 2024-10-24T01:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008048539-BafRegressMetrics 2024-10-24T01:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008100379-CountBases 2024-10-24T01:54:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008205211-DetermineGermlineContigPloidy 2024-10-24T01:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008225435-FindBreakpointEvidenceSpark-BETA 2024-10-24T01:54:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008242715-MappingQuality 2024-10-24T01:54:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008298139-FlowBasedTPAttributeSymetricReadFilter 2024-10-24T01:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008315291-VariantsToTable 2024-10-24T01:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008564763-ClusterCrosscheckMetrics-Picard 2024-10-24T01:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008575771-ClipReads 2024-10-24T01:54:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008620955-ReadGroupHasFlowOrderReadFilter 2024-10-24T01:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008655003-CollectSVEvidence-BETA 2024-10-24T01:54:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008709915-DepthPerAlleleBySample 2024-10-24T01:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008767131-HaplotypeFilteringAnnotation 2024-10-24T01:54:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008905627-GatherBamFiles-Picard 2024-10-24T01:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/30332008950171-CalculateFingerprintMetrics-Picard 2024-10-24T01:55:00Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009117211-CollectAlignmentSummaryMetrics-Picard 2024-10-24T01:55:02Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009156891-AnnotateVcfWithBamDepth 2024-10-24T01:55:03Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009249563-MappedReadFilter 2024-10-24T01:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009807515-NonNFastaSize-Picard 2024-10-24T01:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009871643-BaitBiasDetailMetrics 2024-10-24T01:55:16Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009914395-AccumulateVariantCallingMetrics-Picard 2024-10-24T01:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009931547-IlluminaBasecallsToSam-Picard 2024-10-24T01:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009936795-SVCluster-BETA 2024-10-24T01:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/30332009953051-ScoreVariantAnnotations-BETA 2024-10-24T01:55:18Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010233755-ReplaceSamHeader-Picard 2024-10-24T01:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010316059-JexlExpressionReadTagValueFilter 2024-10-24T01:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010583707-MergeBamAlignment-Picard 2024-10-24T01:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010643867-DuplicationMetrics 2024-10-24T01:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010670747-ExtractIlluminaBarcodes-Picard 2024-10-24T01:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010698779-AmbiguousBaseReadFilter 2024-10-24T01:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010734875-RemoveNearbyIndels 2024-10-24T01:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010771227-CollectRawWgsMetrics-Picard 2024-10-24T01:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010796571-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2024-10-24T01:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332010877339-VcfToAdpc-Picard 2024-10-24T01:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011006619-CheckReferenceCompatibility-EXPERIMENTAL 2024-10-24T01:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011028251-ReorderSam-Picard 2024-10-24T01:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011079579-PSScoreMetrics 2024-10-24T01:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011267355-BaseRecalibrator 2024-10-24T01:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011311259-GenotypeConcordanceDetailMetrics 2024-10-24T01:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011362459-ClippingRankSumTest 2024-10-24T01:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011373851-VariantCallingDetailMetrics 2024-10-24T01:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011420571-BQSRPipelineSpark-BETA 2024-10-24T01:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011441563-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2024-10-24T01:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011460507-ArraysVariantCallingDetailMetrics 2024-10-24T01:55:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011522971-CollectInsertSizeMetricsSpark-BETA 2024-10-24T01:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011620891-IntervalListToBed-Picard 2024-10-24T01:55:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011672091-UpdateVcfSequenceDictionary-Picard 2024-10-24T01:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011710235-ExtractVariantAnnotations-BETA 2024-10-24T01:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011862171-PlatformReadFilter 2024-10-24T01:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/30332011989659-SVAnnotate 2024-10-24T01:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012074779-TheoreticalSensitivityMetrics 2024-10-24T01:56:04Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012224539-CollectGcBiasMetrics-Picard 2024-10-24T01:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012241051-LiftoverVcf-Picard 2024-10-24T01:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012388251-MateOnSameContigOrNoMappedMateReadFilter 2024-10-24T01:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012456603-ApplyBQSRSpark-BETA 2024-10-24T01:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012538907-CollectMultipleMetrics-Picard 2024-10-24T01:56:10Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012568859-WellformedFlowBasedReadFilter 2024-10-24T01:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012614555-ExtractSVEvidenceSpark-BETA 2024-10-24T01:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012671003-MethylationTypeCaller-EXPERIMENTAL 2024-10-24T01:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012931739-FlowBasedTPAttributeValidReadFilter 2024-10-24T01:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/30332012991003-WgsMetrics 2024-10-24T01:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013076251-ConvertHeaderlessHadoopBamShardToBam-BETA 2024-10-24T01:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013101083-CollectRnaSeqMetrics-Picard 2024-10-24T01:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013145115-PathSeqScoreSpark 2024-10-24T01:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013170843-SplitReads 2024-10-24T01:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013389339-IntervalOverlapReadFilter 2024-10-24T01:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013482395-PathSeqFilterSpark 2024-10-24T01:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013551515-PlotDenoisedCopyRatios 2024-10-24T01:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013623835-FastaAlternateReferenceMaker 2024-10-24T01:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013692059-StructuralVariationDiscoveryPipelineSpark-BETA 2024-10-24T01:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013831707-CigarContainsNoNOperator 2024-10-24T01:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013890715-SplitSamByLibrary-Picard 2024-10-24T01:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013917211-CrosscheckFingerprints-Picard 2024-10-24T01:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332013968411-TandemRepeat 2024-10-24T01:56:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30332014058523-AS-QualByDepth 2024-10-24T01:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332014187803-FindMendelianViolations-Picard 2024-10-24T01:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332014273051-IndexFeatureFile 2024-10-24T01:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332014350875-QualityScoreDistributionSpark-BETA 2024-10-24T01:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332014617755-CollectOxoGMetrics-Picard 2024-10-24T01:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30332014656155-CountReadsSpark 2024-10-24T01:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332014813851-CheckTerminatorBlock-Picard 2024-10-24T01:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332018463643-NonChimericOriginalAlignmentReadFilter 2024-10-24T01:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332018478107-MeanQualityByCycle-Picard 2024-10-24T01:54:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332018626843-NotProperlyPairedReadFilter 2024-10-24T01:54:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332018805787-Funcotator 2024-10-24T01:54:29Z https://gatk.broadinstitute.org/hc/en-us/articles/30332018841627-CollectQualityYieldMetrics-Picard 2024-10-24T01:54:29Z https://gatk.broadinstitute.org/hc/en-us/articles/30332019053723-VariantEval-BETA 2024-10-24T01:54:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30332019232027-GnarlyGenotyper-BETA 2024-10-24T01:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332019284763-EstimateLibraryComplexity-Picard 2024-10-24T01:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332019495067-BaseDistributionByCycleMetrics 2024-10-24T01:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332019513755-OverlappingErrorMetric 2024-10-24T01:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332019524763-BamToBfq-Picard 2024-10-24T01:54:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332019965083-FlowFeatureMapper-EXPERIMENTAL 2024-10-24T01:54:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332020227483-PostProcessReadsForRSEM-BETA 2024-10-24T01:54:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30332020259355-GeneExpressionEvaluation-BETA 2024-10-24T01:54:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332020683931-BaitBiasSummaryMetrics 2024-10-24T01:54:59Z https://gatk.broadinstitute.org/hc/en-us/articles/30332020903067-GenotypeConcordanceContingencyMetrics 2024-10-24T01:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/30332021284891-SortSamSpark-BETA 2024-10-24T01:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/30332021414683-GetNormalArtifactData 2024-10-24T01:55:11Z https://gatk.broadinstitute.org/hc/en-us/articles/30332021479579-SplitSamByNumberOfReads-Picard 2024-10-24T01:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/30332021530011-ComposeSTRTableFile 2024-10-24T01:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/30332021620379-FilterMutectCalls 2024-10-24T01:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/30332021749275-SelectVariants 2024-10-24T01:55:17Z https://gatk.broadinstitute.org/hc/en-us/articles/30332021917723-CollectQualityYieldMetricsSpark-BETA 2024-10-24T01:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/30332022066459-HmerQualitySymetricReadFilter 2024-10-24T01:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30332022097179-MateDistantReadFilter 2024-10-24T01:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/30332022249371-ClusteredCrosscheckMetric 2024-10-24T01:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30332022344603-MarkIlluminaAdapters-Picard 2024-10-24T01:55:29Z https://gatk.broadinstitute.org/hc/en-us/articles/30332022870939-HmerIndelLength 2024-10-24T01:55:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332022936475-MarkDuplicates-Picard 2024-10-24T01:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332023921051-GatherBQSRReports 2024-10-24T01:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/30332023942555-CalculateContamination 2024-10-24T01:55:05Z https://gatk.broadinstitute.org/hc/en-us/articles/30332024106395-StrandBiasBySample 2024-10-24T01:55:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30332024150171-CollectReadCounts 2024-10-24T01:55:09Z https://gatk.broadinstitute.org/hc/en-us/articles/30332024333979-HaplotypeCallerSpark-BETA 2024-10-24T01:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/30332024349211-CollectJumpingLibraryMetrics-Picard 2024-10-24T01:55:12Z https://gatk.broadinstitute.org/hc/en-us/articles/30332024680091-MappingQualityReadFilter 2024-10-24T01:55:19Z https://gatk.broadinstitute.org/hc/en-us/articles/30332024760603-CreateBafRegressMetricsFile-Picard 2024-10-24T01:55:20Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025034267-MateUnmappedAndUnmappedReadFilter 2024-10-24T01:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025126939-SetNmAndUqTags-Picard 2024-10-24T01:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025317403-CollectTargetedPcrMetrics-Picard 2024-10-24T01:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025375003-ReblockGVCF 2024-10-24T01:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025439387-FixMisencodedBaseQualityReads 2024-10-24T01:55:35Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025514267-RevertSamSpark-BETA 2024-10-24T01:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025699995-OriginalAlignment 2024-10-24T01:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025803163-AllelePseudoDepth 2024-10-24T01:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332025974427-FilterAlignmentArtifacts-EXPERIMENTAL 2024-10-24T01:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332026100251-ExcessHet 2024-10-24T01:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332026215195-DownsampleSam-Picard 2024-10-24T01:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332026391963-IndelClassify 2024-10-24T01:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332026501659-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2024-10-24T01:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30332026547995-ApplyVQSR 2024-10-24T01:55:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30332026703003-MappingQualityZero 2024-10-24T01:55:58Z https://gatk.broadinstitute.org/hc/en-us/articles/30332026757915-CallCopyRatioSegments 2024-10-24T01:55:58Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027027227-VcfFormatConverter-Picard 2024-10-24T01:56:03Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027051035-AddOrReplaceReadGroups-Picard 2024-10-24T01:56:03Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027102875-LocalAssembler-BETA 2024-10-24T01:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027403291-ReadTagValueFilter 2024-10-24T01:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027430555-ReadPosition 2024-10-24T01:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027487771-TargetedPcrMetrics 2024-10-24T01:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027857819-IlluminaPhasingMetrics 2024-10-24T01:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027874203-InbreedingCoeff 2024-10-24T01:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027892251-GtfToBed 2024-10-24T01:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027911835-ReadLengthEqualsCigarLengthReadFilter 2024-10-24T01:56:17Z https://gatk.broadinstitute.org/hc/en-us/articles/30332027999515-IndependentReplicateMetric 2024-10-24T01:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/30332028160667-MergeSamFiles-Picard 2024-10-24T01:56:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332028207515-AnnotateIntervals 2024-10-24T01:56:25Z https://gatk.broadinstitute.org/hc/en-us/articles/30332028375963-BaseQuality 2024-10-24T01:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332028468635-CollectBaseDistributionByCycleSpark-BETA 2024-10-24T01:56:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30332029175451-BuildBamIndex-Picard 2024-10-24T01:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332029484187-DepthPerSampleHC 2024-10-24T01:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332030089115-HmerMotifs 2024-10-24T01:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30332030143899-ReadLengthReadFilter 2024-10-24T01:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332032207771-JumpingLibraryMetrics 2024-10-24T01:54:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332032425371-NotDuplicateReadFilter 2024-10-24T01:54:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332032605467-MergePedIntoVcf-Picard 2024-10-24T01:54:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332032682267-CompareReferences-EXPERIMENTAL 2024-10-24T01:54:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332032753563-MendelianViolationMetrics 2024-10-24T01:54:45Z https://gatk.broadinstitute.org/hc/en-us/articles/30332033020187-NormalizeFasta-Picard 2024-10-24T01:54:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332033059355-PFFailSummaryMetric 2024-10-24T01:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332033101851-UpdateVCFSequenceDictionary 2024-10-24T01:54:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332033330971-GetSampleName 2024-10-24T01:54:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30332033465243-SetNmMdAndUqTags-Picard 2024-10-24T01:54:58Z https://gatk.broadinstitute.org/hc/en-us/articles/30332033872923-ExtractSequences-Picard 2024-10-24T01:55:04Z https://gatk.broadinstitute.org/hc/en-us/articles/30332034285851-FilterIntervals 2024-10-24T01:55:10Z https://gatk.broadinstitute.org/hc/en-us/articles/30332034495771-MateDifferentStrandReadFilter 2024-10-24T01:55:14Z https://gatk.broadinstitute.org/hc/en-us/articles/30332034903323-CreateHadoopBamSplittingIndex-BETA 2024-10-24T01:55:21Z https://gatk.broadinstitute.org/hc/en-us/articles/30332034969499-BwaAndMarkDuplicatesPipelineSpark-BETA 2024-10-24T01:55:23Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035078811-CountFalsePositives-BETA 2024-10-24T01:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035108251-CollectIlluminaLaneMetrics-Picard 2024-10-24T01:55:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035279003-MatchingBasesAndQualsReadFilter 2024-10-24T01:55:30Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035311131-MeanQualityByCycleSpark-BETA 2024-10-24T01:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035400603-CollectBaseDistributionByCycle-Picard 2024-10-24T01:55:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035453467-RrbsCpgDetailMetrics 2024-10-24T01:55:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035607323-PFFailDetailedMetric 2024-10-24T01:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035821723-GcContent 2024-10-24T01:55:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332035978395-PositionBasedDownsampleSam-Picard 2024-10-24T01:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332036036379-RawWgsMetrics 2024-10-24T01:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332036098203-FlagStatSpark 2024-10-24T01:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/30332036200731-GetPileupSummaries 2024-10-24T01:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30332036263451-LikelihoodRankSumTest 2024-10-24T01:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30332036853275-ReadNameReadFilter 2024-10-24T01:55:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332036961947-ErrorSummaryMetrics 2024-10-24T01:55:58Z https://gatk.broadinstitute.org/hc/en-us/articles/30332038544795-CpcgMetrics 2024-10-24T01:56:13Z https://gatk.broadinstitute.org/hc/en-us/articles/30332038740379-BaitDesigner-Picard 2024-10-24T01:56:16Z https://gatk.broadinstitute.org/hc/en-us/articles/30332038873755-FixMateInformation-Picard 2024-10-24T01:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/30332038947995-BpmToNormalizationManifestCsv-Picard 2024-10-24T01:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039049499-SortSam-Picard 2024-10-24T01:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039213339-PassesVendorQualityCheckReadFilter 2024-10-24T01:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039339291-ReadPosRankSumTest 2024-10-24T01:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039425051-NonZeroReferenceLengthAlignmentReadFilter 2024-10-24T01:56:29Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039449755-GroundTruthReadsBuilder-EXPERIMENTAL 2024-10-24T01:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039543323-SVConcordance-BETA 2024-10-24T01:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039815195-BaseErrorMetric 2024-10-24T01:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/30332039882779-SplitVcfs-Picard 2024-10-24T01:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040065435-FindBadGenomicKmersSpark-BETA 2024-10-24T01:56:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040138523-AnalyzeSaturationMutagenesis-BETA 2024-10-24T01:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040239771-Concordance 2024-10-24T01:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040404635-NotSecondaryAlignmentReadFilter 2024-10-24T01:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040592539-MappingQualityRankSumTest 2024-10-24T01:55:10Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040605211-MappingQualityNotZeroReadFilter 2024-10-24T01:55:11Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040690203-HsMetrics 2024-10-24T01:55:13Z https://gatk.broadinstitute.org/hc/en-us/articles/30332040770715-FingerprintMetrics 2024-10-24T01:55:15Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041038491-PrintReads 2024-10-24T01:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041045275-GenotypeConcordanceSummaryMetrics 2024-10-24T01:55:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041116315-AlignmentSummaryMetrics 2024-10-24T01:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041129243-ValidAlignmentStartReadFilter 2024-10-24T01:55:24Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041140507-ReadsPipelineSpark-BETA 2024-10-24T01:55:25Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041216923-CountBasesInReference 2024-10-24T01:55:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041282075-VcfToIntervalList-Picard 2024-10-24T01:55:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041398043-FragmentLength 2024-10-24T01:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041409563-CheckIlluminaDirectory-Picard 2024-10-24T01:55:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041497755-TrainVariantAnnotationsModel-BETA 2024-10-24T01:55:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041567003-ModelSegments 2024-10-24T01:55:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041718043-CompareDuplicatesSpark-BETA 2024-10-24T01:55:38Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041832731-CreateSequenceDictionary-Picard 2024-10-24T01:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30332041910683-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2024-10-24T01:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042005403-PreAdapterDetailMetrics 2024-10-24T01:55:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042095515-GenotypeSummaries 2024-10-24T01:55:45Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042161179-PairedReadFilter 2024-10-24T01:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042223387-VariantFiltration 2024-10-24T01:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042471835-PossibleDeNovo 2024-10-24T01:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042500379-GroundTruthScorer-EXPERIMENTAL 2024-10-24T01:55:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042623131-GermlineCNVCaller 2024-10-24T01:55:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042807707-CollectQualityYieldMetricsSNVQ-Picard 2024-10-24T01:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/30332042880027-IlluminaLaneMetrics 2024-10-24T01:56:00Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043223963-ArraysVariantCallingSummaryMetrics 2024-10-24T01:56:06Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043243675-AddOATag-Picard 2024-10-24T01:56:07Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043349147-ReadStrandFilter 2024-10-24T01:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043510171-IndelLength 2024-10-24T01:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043557147-CollectAllelicCounts 2024-10-24T01:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043631387-PreprocessIntervals 2024-10-24T01:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043703707-FlagStat 2024-10-24T01:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043720603-CombineGenotypingArrayVcfs-Picard 2024-10-24T01:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043836059-PrintVariantsSpark 2024-10-24T01:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043889179-FastqToSam-Picard 2024-10-24T01:56:20Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043930523-SamToFastq-Picard 2024-10-24T01:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30332043983259-GcBiasDetailMetrics 2024-10-24T01:56:22Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044011291-CollectIlluminaBasecallingMetrics-Picard 2024-10-24T01:56:23Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044076059-GatherVcfsCloud 2024-10-24T01:56:25Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044115227-RevertSam-Picard 2024-10-24T01:56:26Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044204955-AS-MappingQualityRankSumTest 2024-10-24T01:56:27Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044447003-SplitIntervals 2024-10-24T01:56:33Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044480411-CycleSkipStatus 2024-10-24T01:56:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044600603-DepthOfCoverage-BETA 2024-10-24T01:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044640411-ProperlyPairedReadFilter 2024-10-24T01:56:38Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044749979-GenotypeGVCFs 2024-10-24T01:56:40Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044942491-CollectRrbsMetrics-Picard 2024-10-24T01:56:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332044996891-WgsMetricsWithNonZeroCoverage 2024-10-24T01:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045335323-AlleleFraction 2025-01-16T19:52:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045418267-AssemblyComplexity 2024-10-24T01:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045459611-CountNs 2024-10-24T01:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045597467-CreateReadCountPanelOfNormals 2024-10-24T01:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045639835-CountBasesSpark 2024-10-24T01:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045721883-CheckPileup 2024-10-24T01:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045734555-GtcToVcf-Picard 2024-10-24T01:56:56Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045759387-QualityYieldMetrics 2024-10-24T01:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332045790747-CleanSam-Picard 2024-10-24T01:56:57Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057424667-BedToIntervalList-Picard 2024-10-24T01:55:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057608603-GoodCigarReadFilter 2024-10-24T01:55:41Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057693083-TransmittedSingleton 2024-10-24T01:55:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057809179-PostprocessGermlineCNVCalls 2024-10-24T01:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057839003-NotSupplementaryAlignmentReadFilter 2024-10-24T01:55:44Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057906971-CollectWgsMetrics-Picard 2024-10-24T01:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057926683-UmiMetrics 2024-10-24T01:55:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057956251-AS-ReadPosRankSumTest 2024-10-24T01:55:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30332057987611-FifoBuffer-Picard 2024-10-24T01:55:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058075035-RevertBaseQualityScores 2024-10-24T01:55:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058110619-GatherTranches-BETA 2024-10-24T01:55:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058185115-CompareSAMs-Picard 2024-10-24T01:55:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058270747-TransferReadTags-EXPERIMENTAL 2024-10-24T01:55:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058362011-DenoiseReadCounts 2024-10-24T01:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058380827-BaseQualityRankSumTest 2024-10-24T01:55:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058662171-ScatterIntervalsByNs-Picard 2024-10-24T01:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058704795-AS-InbreedingCoeff 2024-10-24T01:55:59Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058799003-Mutect2 2024-10-24T01:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058823067-CollectArraysVariantCallingMetrics-Picard 2024-10-24T01:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058894107-VariantType 2024-10-24T01:56:02Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058945691-PlotModeledSegments 2024-10-24T01:56:03Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058952859-CollectVariantCallingMetrics-Picard 2024-10-24T01:56:04Z https://gatk.broadinstitute.org/hc/en-us/articles/30332058987163-CombineGVCFs 2024-10-24T01:56:04Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059027995-PrintReadCounts-EXPERIMENTAL 2024-10-24T01:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059055643-QualityYieldMetricsFlow 2024-10-24T01:56:05Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059304603-Coverage 2024-10-24T01:56:08Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059396507-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2024-10-24T01:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059416859-CalculateGenotypePosteriors 2024-10-24T01:56:09Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059651483-QualityScoreDistribution-Picard 2024-10-24T01:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059673371-PrintDistantMates 2024-10-24T01:56:15Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059803931-SortVcf-Picard 2024-10-24T01:56:18Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059832987-ValidateSamFile-Picard 2024-10-24T01:56:19Z https://gatk.broadinstitute.org/hc/en-us/articles/30332059899547-ReadGroupBlackListReadFilter 2024-10-24T01:56:21Z https://gatk.broadinstitute.org/hc/en-us/articles/30332060377627-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2024-10-24T01:56:32Z https://gatk.broadinstitute.org/hc/en-us/articles/30332060475419-UnmarkDuplicates 2024-10-24T01:56:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30332060526235-EvaluateInfoFieldConcordance-BETA 2024-10-24T01:56:35Z https://gatk.broadinstitute.org/hc/en-us/articles/30332060553115-NonZeroFragmentLengthReadFilter 2024-10-24T01:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332060632731-PileupSpark-BETA 2024-10-24T01:56:37Z https://gatk.broadinstitute.org/hc/en-us/articles/30332060937883-AS-BaseQualityRankSumTest 2024-10-24T01:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332061122331-ShiftFasta-BETA 2024-10-24T01:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332061439003-ConvertSequencingArtifactToOxoG-Picard 2024-10-24T01:56:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30332061644059-RenameSampleInVcf-Picard 2024-10-24T01:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332061809947-PrintReadsSpark 2024-10-24T01:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30332061886619-FilterVariantTranches 2024-10-24T01:56:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30332074681115-BamIndexStats-Picard 2024-10-24T01:56:00Z https://gatk.broadinstitute.org/hc/en-us/articles/30332074826907-TargetMetrics 2024-10-24T01:56:01Z https://gatk.broadinstitute.org/hc/en-us/articles/30332075730203-MergeVcfs-Picard 2024-10-24T01:56:10Z https://gatk.broadinstitute.org/hc/en-us/articles/30332075857819-ValidateVariants 2024-10-24T01:56:11Z https://gatk.broadinstitute.org/hc/en-us/articles/30332075938587-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2024-10-24T01:56:12Z https://gatk.broadinstitute.org/hc/en-us/articles/30332076015131-FingerprintingSummaryMetrics 2024-10-24T01:56:14Z https://gatk.broadinstitute.org/hc/en-us/articles/30332076569883-FuncotatorDataSourceDownloader 2024-10-24T01:56:23Z https://gatk.broadinstitute.org/hc/en-us/articles/30332076841243-SeqIsStoredReadFilter 2024-10-24T01:56:28Z https://gatk.broadinstitute.org/hc/en-us/articles/30332076891163-RampedHaplotypeCaller-EXPERIMENTAL 2024-10-24T01:56:30Z https://gatk.broadinstitute.org/hc/en-us/articles/30332076921755-VariantRecalibrator 2024-10-24T01:56:31Z https://gatk.broadinstitute.org/hc/en-us/articles/30332077124635-HmerIndelNuc 2024-10-24T01:56:34Z https://gatk.broadinstitute.org/hc/en-us/articles/30332077175963-SplitNCigarReads 2024-10-24T01:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332077197211-JointGermlineCNVSegmentation-BETA 2024-10-24T01:56:36Z https://gatk.broadinstitute.org/hc/en-us/articles/30332077385627-FilterFuncotations-EXPERIMENTAL 2024-10-24T01:56:39Z https://gatk.broadinstitute.org/hc/en-us/articles/30332077564315-AddCommentsToBam-Picard 2024-10-24T01:56:42Z https://gatk.broadinstitute.org/hc/en-us/articles/30332077752475-FragmentLengthReadFilter 2024-10-24T01:56:43Z https://gatk.broadinstitute.org/hc/en-us/articles/30332077973659-IndelErrorMetric 2024-10-24T01:56:45Z https://gatk.broadinstitute.org/hc/en-us/articles/30332078034075-ReferenceBases 2024-10-24T01:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332078494107-ReadAnonymizer-EXPERIMENTAL 2024-10-24T01:56:51Z https://gatk.broadinstitute.org/hc/en-us/articles/30332078666267-ASEReadCounter 2024-10-24T01:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30332078729883-CreateSomaticPanelOfNormals-BETA 2024-10-24T01:56:55Z https://gatk.broadinstitute.org/hc/en-us/articles/30332090921755-MetricsReadFilter 2024-10-24T01:56:46Z https://gatk.broadinstitute.org/hc/en-us/articles/30332090943259-ValidAlignmentEndReadFilter 2024-10-24T01:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30332090958747-FingerprintingDetailMetrics 2024-10-24T01:56:47Z https://gatk.broadinstitute.org/hc/en-us/articles/30332090985883-FastaReferenceMaker 2024-10-24T01:56:48Z https://gatk.broadinstitute.org/hc/en-us/articles/30332091159323-OrientationBiasReadCounts 2024-10-24T01:56:49Z https://gatk.broadinstitute.org/hc/en-us/articles/30332091291547-InsertSizeMetrics 2024-10-24T01:56:50Z https://gatk.broadinstitute.org/hc/en-us/articles/30332091369115-MappingQualityAvailableReadFilter 2024-10-24T01:56:52Z https://gatk.broadinstitute.org/hc/en-us/articles/30332091453339-CollectDuplicateMetrics-Picard 2024-10-24T01:56:53Z https://gatk.broadinstitute.org/hc/en-us/articles/30332091548443-CalibrateDragstrModel 2024-10-24T01:56:54Z https://gatk.broadinstitute.org/hc/en-us/articles/30932945361691-An-announcement-about-temporary-changes-to-the-moderation-of-GATK-forum-and-how-it-affects-our-users 2026-02-10T04:14:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967422067099-NonChimericOriginalAlignmentReadFilter 2025-04-14T14:18:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967428225179-BwaMemIndexImageCreator 2025-04-14T14:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967428300699-VerifyIDIntensityContaminationMetrics 2025-04-14T14:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967428377883-NotProperlyPairedReadFilter 2025-04-14T14:18:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967428601627-BarcodeMetric 2025-04-14T14:18:21Z https://gatk.broadinstitute.org/hc/en-us/articles/35967428706971-WellformedReadFilter 2025-04-14T14:18:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967428775323-SampleReadFilter 2025-04-14T14:18:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967429156891-Funcotator 2025-04-14T14:18:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967429967259-GcBiasSummaryMetrics 2025-04-14T14:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967430723483-PrintReadsHeader 2025-04-14T14:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967430958363-CountVariants 2025-04-14T14:18:32Z https://gatk.broadinstitute.org/hc/en-us/articles/35967431019931-AllowAllReadsReadFilter 2025-04-14T14:18:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967431072667-LiftOverIntervalList-Picard 2025-04-14T14:18:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967431252507-OverlappingErrorMetric 2025-04-14T14:18:34Z https://gatk.broadinstitute.org/hc/en-us/articles/35967431314971-BamToBfq-Picard 2025-04-14T14:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967431481755-PreAdapterSummaryMetrics 2025-04-14T14:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967431807771-MergePedIntoVcf-Picard 2025-04-14T14:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967441484827-CollectIndependentReplicateMetrics-Picard-EXPERIMENTAL 2025-04-14T14:18:16Z https://gatk.broadinstitute.org/hc/en-us/articles/35967441582747-ChromosomeCounts 2025-04-14T14:18:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967441662491-LibraryReadFilter 2025-04-14T14:18:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967441785371-CollectWgsMetricsWithNonZeroCoverage-Picard-EXPERIMENTAL 2025-04-14T14:18:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967443026715-RMSMappingQuality 2025-04-14T14:18:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967443684891-AlignmentAgreesWithHeaderReadFilter 2025-04-14T14:18:26Z https://gatk.broadinstitute.org/hc/en-us/articles/35967444109851-RnaSeqMetrics 2025-04-14T14:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967444918939-ErrorMetric 2025-04-14T14:18:32Z https://gatk.broadinstitute.org/hc/en-us/articles/35967445254043-BaseDistributionByCycleMetrics 2025-04-14T14:18:34Z https://gatk.broadinstitute.org/hc/en-us/articles/35967445410459-VariantCallingSummaryMetrics 2025-04-14T14:18:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967445632667-VariantAnnotator 2025-04-14T14:18:36Z https://gatk.broadinstitute.org/hc/en-us/articles/35967453385499-MeanQualityByCycle-Picard 2025-04-14T14:18:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967453600539-CollectHiSeqXPfFailMetrics-Picard 2025-04-14T14:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967453768347-GenotypeConcordance-Picard 2025-04-14T14:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967454697371-ExcessiveEndClippedReadFilter 2025-04-14T14:18:21Z https://gatk.broadinstitute.org/hc/en-us/articles/35967455245595-AnalyzeCovariates 2025-04-14T14:18:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967455968923-CollectQualityYieldMetrics-Picard 2025-04-14T14:18:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967456109595-PathSeqPipelineSpark 2025-04-14T14:18:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967456995355-FilterVcf-Picard 2025-04-14T14:18:26Z https://gatk.broadinstitute.org/hc/en-us/articles/35967468118427-DumpTabixIndex 2025-04-14T14:18:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967468595995-Pileup 2025-04-14T14:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967468676635-OverclippedReadFilter 2025-04-14T14:18:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967469400987-FirstOfPairReadFilter 2025-04-14T14:18:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967469749403-CalcMetadataSpark-BETA 2025-04-14T14:18:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967469858459-SecondOfPairReadFilter 2025-04-14T14:18:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967470004891-AS-StrandOddsRatio 2025-04-14T14:18:26Z https://gatk.broadinstitute.org/hc/en-us/articles/35967470168987-ParallelCopyGCSDirectoryIntoHDFSSpark-BETA 2025-04-14T14:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967470492955-CountReads 2025-04-14T14:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967470817947-IlluminaBasecallingMetrics 2025-04-14T14:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967471322267-AnnotateVcfWithExpectedAlleleFraction 2025-04-14T14:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967471659675-NotDuplicateReadFilter 2025-04-14T14:18:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967472150427-ArraysControlCodesSummaryMetrics 2025-04-14T14:18:36Z https://gatk.broadinstitute.org/hc/en-us/articles/35967472300187-FilterSamReads-Picard 2025-04-14T14:18:36Z https://gatk.broadinstitute.org/hc/en-us/articles/35967472536859-BafRegressMetrics 2025-04-14T14:18:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967474883099-AccumulateQualityYieldMetrics-Picard 2025-04-14T14:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967475130779-JumpingLibraryMetrics 2025-04-14T14:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967476590107-PrimaryLineReadFilter 2025-04-14T14:18:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967476702747-CollectMultipleMetricsSpark-BETA 2025-04-14T14:18:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967489978907-AlleleFrequencyQCMetric 2025-04-14T14:18:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967490357915-PFFailSummaryMetric 2025-04-14T14:18:46Z https://gatk.broadinstitute.org/hc/en-us/articles/35967490496283-UpdateVCFSequenceDictionary 2025-04-14T14:18:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967490807579-VariantEval-BETA 2025-04-14T14:18:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967491463067-FixVcfHeader-Picard 2025-04-14T14:18:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967491694107-CollectHsMetrics-Picard 2025-04-14T14:18:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967492186395-GnarlyGenotyper-BETA 2025-04-14T14:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967492497819-EstimateLibraryComplexity-Picard 2025-04-14T14:18:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967503097499-HasReadGroupReadFilter 2025-04-14T14:18:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967503594651-FlowBasedTPAttributeSymetricReadFilter 2025-04-14T14:18:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967503965339-NormalizeFasta-Picard 2025-04-14T14:18:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967504403611-SamFormatConverter-Picard 2025-04-14T14:18:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967504777371-CollectSamErrorMetrics-Picard 2025-04-14T14:18:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967505484827-SiteDepthtoBAF-EXPERIMENTAL 2025-04-14T14:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967505634331-MarkDuplicatesSpark 2025-04-14T14:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967512751515--Tool-Documentation-Index 2025-04-14T14:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967512817179-MendelianViolationMetrics 2025-04-14T14:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967512868891-CheckFingerprint-Picard 2025-04-14T14:18:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967513157275-UniqueAltReadCount 2025-04-14T14:18:42Z https://gatk.broadinstitute.org/hc/en-us/articles/35967513360155-QualByDepth 2025-04-14T14:18:42Z https://gatk.broadinstitute.org/hc/en-us/articles/35967513433243-FlowFeatureMapper-EXPERIMENTAL 2025-04-14T14:18:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967513593627-VariantsToTable 2025-04-14T14:18:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967514132507-CountVariantsSpark 2025-04-14T14:18:46Z https://gatk.broadinstitute.org/hc/en-us/articles/35967514993435-SoftClippedReadFilter 2025-04-14T14:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/35967515832603-ViewSam-Picard 2025-04-14T14:18:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967524940699-StrandOddsRatio 2025-04-14T14:18:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967525616027-DetermineGermlineContigPloidy 2025-04-14T14:18:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967525745691-FindBreakpointEvidenceSpark-BETA 2025-04-14T14:18:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967526041627-MappingQuality 2025-04-14T14:18:42Z https://gatk.broadinstitute.org/hc/en-us/articles/35967526829595-AddFlowSNVQuality-EXPERIMENTAL 2025-04-14T14:18:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967527012891-HaplotypeBasedVariantRecaller-EXPERIMENTAL 2025-04-14T14:18:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967527273755-AS-RMSMappingQuality 2025-04-14T14:18:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967528413083-GeneExpressionEvaluation-BETA 2025-04-14T14:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967529626395-GetSampleName 2025-04-14T14:18:51Z https://gatk.broadinstitute.org/hc/en-us/articles/35967530268443-CollectSVEvidence-BETA 2025-04-14T14:18:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967531518747-CalculateReadGroupChecksum-Picard 2025-04-14T14:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967531724187-GcBiasMetrics 2025-04-14T14:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967532280603-CompareBaseQualities 2025-04-14T14:18:57Z https://gatk.broadinstitute.org/hc/en-us/articles/35967532460827-SamComparisonMetric 2025-04-14T14:18:58Z https://gatk.broadinstitute.org/hc/en-us/articles/35967533533083-CompareReferences-EXPERIMENTAL 2025-04-14T14:18:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967533607579-CountBases 2025-04-14T14:18:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967535320859-IlluminaBasecallsToFastq-Picard 2025-04-14T14:18:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967535433115-PostProcessReadsForRSEM-BETA 2025-04-14T14:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967535518107-FisherStrand 2025-04-14T14:18:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967535929755-ReadGroupHasFlowOrderReadFilter 2025-04-14T14:18:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967537532059-FuncotateSegments-BETA 2025-04-14T14:18:55Z https://gatk.broadinstitute.org/hc/en-us/articles/35967537725083-CalculateFingerprintMetrics-Picard 2025-04-14T14:18:56Z https://gatk.broadinstitute.org/hc/en-us/articles/35967538178331-CollectAlignmentSummaryMetrics-Picard 2025-04-14T14:18:58Z https://gatk.broadinstitute.org/hc/en-us/articles/35967539031707-CpxVariantReInterpreterSpark-BETA 2025-04-14T14:19:03Z https://gatk.broadinstitute.org/hc/en-us/articles/35967539535515-LearnReadOrientationModel 2025-04-14T14:19:05Z https://gatk.broadinstitute.org/hc/en-us/articles/35967541210139-ClusterCrosscheckMetrics-Picard 2025-04-14T14:18:49Z https://gatk.broadinstitute.org/hc/en-us/articles/35967541270683-ClipReads 2025-04-14T14:18:49Z https://gatk.broadinstitute.org/hc/en-us/articles/35967541317915-PSFilterMetrics 2025-04-14T14:18:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967542440987-DepthPerAlleleBySample 2025-04-14T14:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967542766619-HaplotypeFilteringAnnotation 2025-04-14T14:18:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967543137179-BaitBiasSummaryMetrics 2025-04-14T14:18:55Z https://gatk.broadinstitute.org/hc/en-us/articles/35967543278875-PathSeqBuildReferenceTaxonomy 2025-04-14T14:18:56Z https://gatk.broadinstitute.org/hc/en-us/articles/35967543512347-BwaSpark-BETA 2025-04-14T14:18:57Z https://gatk.broadinstitute.org/hc/en-us/articles/35967543702299-AnnotateVcfWithBamDepth 2025-04-14T14:18:58Z https://gatk.broadinstitute.org/hc/en-us/articles/35967543828635-GenotypeConcordanceContingencyMetrics 2025-04-14T14:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/35967543876891-GatherVcfs-Picard 2025-04-14T14:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/35967544009115-ExtractSequences-Picard 2025-04-14T14:19:00Z https://gatk.broadinstitute.org/hc/en-us/articles/35967544091419-MarkDuplicatesWithMateCigar-Picard 2025-04-14T14:19:00Z https://gatk.broadinstitute.org/hc/en-us/articles/35967544160923-GatherBQSRReports 2025-04-14T14:19:01Z https://gatk.broadinstitute.org/hc/en-us/articles/35967544633371-MakeSitesOnlyVcf-Picard 2025-04-14T14:19:03Z https://gatk.broadinstitute.org/hc/en-us/articles/35967544688539-IntervalListTools-Picard 2025-04-14T14:19:04Z https://gatk.broadinstitute.org/hc/en-us/articles/35967545214619-LeftAlignIndels 2025-04-14T14:19:06Z https://gatk.broadinstitute.org/hc/en-us/articles/35967545475483-MappingQualityNotZeroReadFilter 2025-04-14T14:19:07Z https://gatk.broadinstitute.org/hc/en-us/articles/35967545607579-HaplotypeCallerSpark-BETA 2025-04-14T14:19:08Z https://gatk.broadinstitute.org/hc/en-us/articles/35967545691803-CollectJumpingLibraryMetrics-Picard 2025-04-14T14:19:09Z https://gatk.broadinstitute.org/hc/en-us/articles/35967545914139-ComposeSTRTableFile 2025-04-14T14:19:10Z https://gatk.broadinstitute.org/hc/en-us/articles/35967546040731-MateDifferentStrandReadFilter 2025-04-14T14:19:10Z https://gatk.broadinstitute.org/hc/en-us/articles/35967546106395-NonNFastaSize-Picard 2025-04-14T14:19:11Z https://gatk.broadinstitute.org/hc/en-us/articles/35967547297819-CollectQualityYieldMetricsSpark-BETA 2025-04-14T14:19:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967547914267-GenotypeConcordanceSummaryMetrics 2025-04-14T14:19:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967547997595-HmerQualitySymetricReadFilter 2025-04-14T14:19:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967548876443-CountBasesInReference 2025-04-14T14:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967558527131-StrandBiasBySample 2025-04-14T14:19:04Z https://gatk.broadinstitute.org/hc/en-us/articles/35967558778395-SortSamSpark-BETA 2025-04-14T14:19:06Z https://gatk.broadinstitute.org/hc/en-us/articles/35967559436443-HsMetrics 2025-04-14T14:19:09Z https://gatk.broadinstitute.org/hc/en-us/articles/35967559772699-FilterMutectCalls 2025-04-14T14:19:11Z https://gatk.broadinstitute.org/hc/en-us/articles/35967560099739-BaitBiasDetailMetrics 2025-04-14T14:19:12Z https://gatk.broadinstitute.org/hc/en-us/articles/35967560494747-SVCluster-BETA 2025-04-14T14:19:14Z https://gatk.broadinstitute.org/hc/en-us/articles/35967560604571-ScoreVariantAnnotations-BETA 2025-04-14T14:19:15Z https://gatk.broadinstitute.org/hc/en-us/articles/35967560824859-GenomicsDBImport 2025-04-14T14:19:16Z https://gatk.broadinstitute.org/hc/en-us/articles/35967561067803-FlowPairHMMAlignReadsToHaplotypes-EXPERIMENTAL 2025-04-14T14:19:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967561336859-CreateHadoopBamSplittingIndex-BETA 2025-04-14T14:19:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967561938203-ValidAlignmentStartReadFilter 2025-04-14T14:19:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967562085659-ReplaceSamHeader-Picard 2025-04-14T14:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967563182107-DiscoverVariantsFromContigAlignmentsSAMSpark-BETA 2025-04-14T14:19:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967563334427-FragmentLength 2025-04-14T14:19:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967563672347-RrbsSummaryMetrics 2025-04-14T14:19:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967563937947-MergeBamAlignment-Picard 2025-04-14T14:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967564177307-ModelSegments 2025-04-14T14:19:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967564250523-DuplicationMetrics 2025-04-14T14:19:32Z https://gatk.broadinstitute.org/hc/en-us/articles/35967564752795-RemoveNearbyIndels 2025-04-14T14:19:34Z https://gatk.broadinstitute.org/hc/en-us/articles/35967564853531-CompareDuplicatesSpark-BETA 2025-04-14T14:19:34Z https://gatk.broadinstitute.org/hc/en-us/articles/35967565640475-AllelePseudoDepth 2025-04-14T14:19:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967565797915-PositionBasedDownsampleSam-Picard 2025-04-14T14:19:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967565835931-CheckReferenceCompatibility-EXPERIMENTAL 2025-04-14T14:19:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967566631067-SetNmMdAndUqTags-Picard 2025-04-14T14:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967566755227-CompareMetrics-Picard 2025-04-14T14:18:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967566873883-GatherBamFiles-Picard 2025-04-14T14:18:55Z https://gatk.broadinstitute.org/hc/en-us/articles/35967567838363-MappedReadFilter 2025-04-14T14:19:00Z https://gatk.broadinstitute.org/hc/en-us/articles/35967568802843-CollectReadCounts 2025-04-14T14:19:05Z https://gatk.broadinstitute.org/hc/en-us/articles/35967570090011-FingerprintMetrics 2025-04-14T14:19:11Z https://gatk.broadinstitute.org/hc/en-us/articles/35967570188059-BaseRecalibratorSpark-BETA 2025-04-14T14:19:12Z https://gatk.broadinstitute.org/hc/en-us/articles/35967570883995-ReadGroupReadFilter 2025-04-14T14:19:15Z https://gatk.broadinstitute.org/hc/en-us/articles/35967571180059-PlatformUnitReadFilter 2025-04-14T14:19:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967572290843-ReadsPipelineSpark-BETA 2025-04-14T14:19:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967572794779-ClusteredCrosscheckMetric 2025-04-14T14:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967573323035-MatchingBasesAndQualsReadFilter 2025-04-14T14:19:26Z https://gatk.broadinstitute.org/hc/en-us/articles/35967574012443-RrbsCpgDetailMetrics 2025-04-14T14:19:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967574177563-FixMisencodedBaseQualityReads 2025-04-14T14:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967574267035-LeftAlignAndTrimVariants 2025-04-14T14:19:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967582970779-CollectSequencingArtifactMetrics-Picard 2025-04-14T14:18:59Z https://gatk.broadinstitute.org/hc/en-us/articles/35967583678491-PathSeqBuildKmers 2025-04-14T14:19:03Z https://gatk.broadinstitute.org/hc/en-us/articles/35967583944603-CollectInsertSizeMetrics-Picard 2025-04-14T14:19:04Z https://gatk.broadinstitute.org/hc/en-us/articles/35967584130971-FragmentDepthPerAlleleBySample 2025-04-14T14:19:05Z https://gatk.broadinstitute.org/hc/en-us/articles/35967584546203-FilterIntervals 2025-04-14T14:19:07Z https://gatk.broadinstitute.org/hc/en-us/articles/35967584622619-MappingQualityRankSumTest 2025-04-14T14:19:07Z https://gatk.broadinstitute.org/hc/en-us/articles/35967585082139-SplitSamByNumberOfReads-Picard 2025-04-14T14:19:09Z https://gatk.broadinstitute.org/hc/en-us/articles/35967586999835-CreateBafRegressMetricsFile-Picard 2025-04-14T14:19:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967587073691-RawGtCount 2025-04-14T14:19:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967587278491-PrintReads 2025-04-14T14:19:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967587545371-BwaAndMarkDuplicatesPipelineSpark-BETA 2025-04-14T14:19:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967587649691-MateDistantReadFilter 2025-04-14T14:19:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967588242715-CollectIlluminaLaneMetrics-Picard 2025-04-14T14:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967588787739-PathSeqBwaSpark 2025-04-14T14:19:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967588876443-MarkIlluminaAdapters-Picard 2025-04-14T14:19:26Z https://gatk.broadinstitute.org/hc/en-us/articles/35967589357339-CheckIlluminaDirectory-Picard 2025-04-14T14:19:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967589683867-ReblockGVCF 2025-04-14T14:19:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967590267291-RevertSamSpark-BETA 2025-04-14T14:19:32Z https://gatk.broadinstitute.org/hc/en-us/articles/35967590779675-CollectRawWgsMetrics-Picard 2025-04-14T14:19:34Z https://gatk.broadinstitute.org/hc/en-us/articles/35967591036955-OriginalAlignment 2025-04-14T14:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967591174299-GcContent 2025-04-14T14:19:36Z https://gatk.broadinstitute.org/hc/en-us/articles/35967591503387-CalculateMixingFractions 2025-04-14T14:19:12Z https://gatk.broadinstitute.org/hc/en-us/articles/35967592196379-MappingQualityReadFilter 2025-04-14T14:19:15Z https://gatk.broadinstitute.org/hc/en-us/articles/35967594203163-VcfToIntervalList-Picard 2025-04-14T14:19:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967594261403-SetNmAndUqTags-Picard 2025-04-14T14:19:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967595029275-CollectBaseDistributionByCycle-Picard 2025-04-14T14:19:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967595300763-TrainVariantAnnotationsModel-BETA 2025-04-14T14:19:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967595886363-ExtractIlluminaBarcodes-Picard 2025-04-14T14:19:32Z https://gatk.broadinstitute.org/hc/en-us/articles/35967597512091-RawWgsMetrics 2025-04-14T14:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967597579035-PostprocessGermlineCNVCalls 2025-04-14T14:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967597743259-PSScoreMetrics 2025-04-14T14:19:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967598316571-PairedReadFilter 2025-04-14T14:19:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967598922523-LikelihoodRankSumTest 2025-04-14T14:19:46Z https://gatk.broadinstitute.org/hc/en-us/articles/35967599076763-RevertBaseQualityScores 2025-04-14T14:19:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967600435355-AS-FisherStrand 2025-04-14T14:18:56Z https://gatk.broadinstitute.org/hc/en-us/articles/35967601391003-CalculateContamination 2025-04-14T14:19:01Z https://gatk.broadinstitute.org/hc/en-us/articles/35967601482651-ApplyBQSR 2025-04-14T14:19:02Z https://gatk.broadinstitute.org/hc/en-us/articles/35967602736283-GetNormalArtifactData 2025-04-14T14:19:08Z https://gatk.broadinstitute.org/hc/en-us/articles/35967603979419-SelectVariants 2025-04-14T14:19:13Z https://gatk.broadinstitute.org/hc/en-us/articles/35967604104859-AccumulateVariantCallingMetrics-Picard 2025-04-14T14:19:13Z https://gatk.broadinstitute.org/hc/en-us/articles/35967604202907-IlluminaBasecallsToSam-Picard 2025-04-14T14:19:14Z https://gatk.broadinstitute.org/hc/en-us/articles/35967605714075-HaplotypeCaller 2025-04-14T14:19:21Z https://gatk.broadinstitute.org/hc/en-us/articles/35967605802651-AlignmentSummaryMetrics 2025-04-14T14:19:21Z https://gatk.broadinstitute.org/hc/en-us/articles/35967606101275-CountFalsePositives-BETA 2025-04-14T14:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967606156315-MateUnmappedAndUnmappedReadFilter 2025-04-14T14:19:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967606515227-JexlExpressionReadTagValueFilter 2025-04-14T14:19:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967608543131-AmbiguousBaseReadFilter 2025-04-14T14:19:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967608604315-BedToIntervalList-Picard 2025-04-14T14:19:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967609281307-CreateSequenceDictionary-Picard 2025-04-14T14:19:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967609623963-TransmittedSingleton 2025-04-14T14:19:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967610482075-FilterAlignmentArtifacts-EXPERIMENTAL 2025-04-14T14:19:42Z https://gatk.broadinstitute.org/hc/en-us/articles/35967610795291-AS-ReadPosRankSumTest 2025-04-14T14:19:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967611013531-ExcessHet 2025-04-14T14:19:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967611230107-CollectUmiPrevalenceMetrics-Picard-EXPERIMENTAL 2025-04-14T14:19:46Z https://gatk.broadinstitute.org/hc/en-us/articles/35967611833499-DownsampleSam-Picard 2025-04-14T14:19:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967612093595-BQSRPipelineSpark-BETA 2025-04-14T14:19:49Z https://gatk.broadinstitute.org/hc/en-us/articles/35967612384795-IndelClassify 2025-04-14T14:19:51Z https://gatk.broadinstitute.org/hc/en-us/articles/35967612530971-CollectInsertSizeMetricsSpark-BETA 2025-04-14T14:19:51Z https://gatk.broadinstitute.org/hc/en-us/articles/35967613180699-UpdateVcfSequenceDictionary-Picard 2025-04-14T14:19:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967613757467-AS-InbreedingCoeff 2025-04-14T14:19:57Z https://gatk.broadinstitute.org/hc/en-us/articles/35967614757403-LocalAssembler-BETA 2025-04-14T14:20:03Z https://gatk.broadinstitute.org/hc/en-us/articles/35967614940443-CollectGcBiasMetrics-Picard 2025-04-14T14:20:04Z https://gatk.broadinstitute.org/hc/en-us/articles/35967615668251-CreateVerifyIDIntensityContaminationMetricsFile-Picard 2025-04-14T14:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/35967615847835-MergeVcfs-Picard 2025-04-14T14:20:09Z https://gatk.broadinstitute.org/hc/en-us/articles/35967615942683-WellformedFlowBasedReadFilter 2025-04-14T14:20:10Z https://gatk.broadinstitute.org/hc/en-us/articles/35967616158875-ValidateVariants 2025-04-14T14:20:10Z https://gatk.broadinstitute.org/hc/en-us/articles/35967616584347-SampleList 2025-04-14T14:19:26Z https://gatk.broadinstitute.org/hc/en-us/articles/35967616835739-MeanQualityByCycleSpark-BETA 2025-04-14T14:19:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967617072795-CollectTargetedPcrMetrics-Picard 2025-04-14T14:19:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967618159003-PFFailDetailedMetric 2025-04-14T14:19:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967618605851-HmerIndelLength 2025-04-14T14:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967618682395-ValidateBasicSomaticShortMutations-EXPERIMENTAL 2025-04-14T14:19:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967618836635-MarkDuplicates-Picard 2025-04-14T14:19:36Z https://gatk.broadinstitute.org/hc/en-us/articles/35967619033883-VcfToAdpc-Picard 2025-04-14T14:19:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967619087131-GoodCigarReadFilter 2025-04-14T14:19:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967619656859-ReorderSam-Picard 2025-04-14T14:19:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967620292251-CollectWgsMetrics-Picard 2025-04-14T14:19:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967620574107-GetPileupSummaries 2025-04-14T14:19:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967620644635-FifoBuffer-Picard 2025-04-14T14:19:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967621397659-ClippingRankSumTest 2025-04-14T14:19:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967621458587-VariantCallingDetailMetrics 2025-04-14T14:19:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967622435995-GermlineCNVCaller 2025-04-14T14:19:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967622605723-ReadNameReadFilter 2025-04-14T14:19:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967623064219-PlatformReadFilter 2025-04-14T14:19:57Z https://gatk.broadinstitute.org/hc/en-us/articles/35967623127707-IlluminaLaneMetrics 2025-04-14T14:19:57Z https://gatk.broadinstitute.org/hc/en-us/articles/35967623540891-SVAnnotate 2025-04-14T14:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/35967623740699-AddOrReplaceReadGroups-Picard 2025-04-14T14:20:01Z https://gatk.broadinstitute.org/hc/en-us/articles/35967624422811-ArraysVariantCallingSummaryMetrics 2025-04-14T14:20:05Z https://gatk.broadinstitute.org/hc/en-us/articles/35967624479899-AddOATag-Picard 2025-04-14T14:20:05Z https://gatk.broadinstitute.org/hc/en-us/articles/35967624560539-ReadTagValueFilter 2025-04-14T14:20:05Z https://gatk.broadinstitute.org/hc/en-us/articles/35967624708123-Coverage 2025-04-14T14:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/35967624754971-ReadStrandFilter 2025-04-14T14:20:07Z https://gatk.broadinstitute.org/hc/en-us/articles/35967627356315-UmiMetrics 2025-04-14T14:19:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967628370587-GatherTranches-BETA 2025-04-14T14:19:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967628636315-CompareSAMs-Picard 2025-04-14T14:19:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967629470747-IntervalListToBed-Picard 2025-04-14T14:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967629921691-MappingQualityZero 2025-04-14T14:19:55Z https://gatk.broadinstitute.org/hc/en-us/articles/35967630847131-VariantType 2025-04-14T14:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/35967631449499-QualityYieldMetricsFlow 2025-04-14T14:20:03Z https://gatk.broadinstitute.org/hc/en-us/articles/35967631562267-LiftoverVcf-Picard 2025-04-14T14:20:04Z https://gatk.broadinstitute.org/hc/en-us/articles/35967634698651-GenotypeConcordanceDetailMetrics 2025-04-14T14:19:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967635593115-GroundTruthScorer-EXPERIMENTAL 2025-04-14T14:19:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967635788187-SvDiscoverFromLocalAssemblyContigAlignmentsSpark-BETA 2025-04-14T14:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967636353819-ErrorSummaryMetrics 2025-04-14T14:19:55Z https://gatk.broadinstitute.org/hc/en-us/articles/35967636548635-CollectQualityYieldMetricsSNVQ-Picard 2025-04-14T14:19:56Z https://gatk.broadinstitute.org/hc/en-us/articles/35967636854939-Mutect2 2025-04-14T14:19:58Z https://gatk.broadinstitute.org/hc/en-us/articles/35967636949915-CollectArraysVariantCallingMetrics-Picard 2025-04-14T14:19:59Z https://gatk.broadinstitute.org/hc/en-us/articles/35967637511195-TheoreticalSensitivityMetrics 2025-04-14T14:20:02Z https://gatk.broadinstitute.org/hc/en-us/articles/35967637709723-PrintReadCounts-EXPERIMENTAL 2025-04-14T14:20:03Z https://gatk.broadinstitute.org/hc/en-us/articles/35967638083227-ReadPosition 2025-04-14T14:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/35967638805019-CollectMultipleMetrics-Picard 2025-04-14T14:20:09Z https://gatk.broadinstitute.org/hc/en-us/articles/35967638983451-IndelLength 2025-04-14T14:20:10Z https://gatk.broadinstitute.org/hc/en-us/articles/35967639672987-QualityScoreDistribution-Picard 2025-04-14T14:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/35967639725211-PrintDistantMates 2025-04-14T14:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/35967640040603-BaitDesigner-Picard 2025-04-14T14:20:15Z https://gatk.broadinstitute.org/hc/en-us/articles/35967640196507-InbreedingCoeff 2025-04-14T14:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/35967641382427-FuncotatorDataSourceDownloader 2025-04-14T14:20:21Z https://gatk.broadinstitute.org/hc/en-us/articles/35967641774363-SimpleMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2025-04-14T14:19:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967642150939-PreAdapterDetailMetrics 2025-04-14T14:19:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967642415771-NotSupplementaryAlignmentReadFilter 2025-04-14T14:19:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967642553243-GenotypeSummaries 2025-04-14T14:19:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967642638235-FlagStatSpark 2025-04-14T14:19:42Z https://gatk.broadinstitute.org/hc/en-us/articles/35967643467675-VariantFiltration 2025-04-14T14:19:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967643818651-BaseRecalibrator 2025-04-14T14:19:46Z https://gatk.broadinstitute.org/hc/en-us/articles/35967644638235-ArraysVariantCallingDetailMetrics 2025-04-14T14:19:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967645057691-DenoiseReadCounts 2025-04-14T14:19:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967645656987-ExtractVariantAnnotations-BETA 2025-04-14T14:19:55Z https://gatk.broadinstitute.org/hc/en-us/articles/35967646308891-BamIndexStats-Picard 2025-04-14T14:19:58Z https://gatk.broadinstitute.org/hc/en-us/articles/35967646500379-TargetMetrics 2025-04-14T14:19:59Z https://gatk.broadinstitute.org/hc/en-us/articles/35967646924315-CollectVariantCallingMetrics-Picard 2025-04-14T14:20:01Z https://gatk.broadinstitute.org/hc/en-us/articles/35967647029403-CombineGVCFs 2025-04-14T14:20:02Z https://gatk.broadinstitute.org/hc/en-us/articles/35967647603611-MateOnSameContigOrNoMappedMateReadFilter 2025-04-14T14:20:06Z https://gatk.broadinstitute.org/hc/en-us/articles/35967647878555-ApplyBQSRSpark-BETA 2025-04-14T14:20:07Z https://gatk.broadinstitute.org/hc/en-us/articles/35967649741723-FixMateInformation-Picard 2025-04-14T14:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/35967649811739-SortVcf-Picard 2025-04-14T14:20:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967649990811-UmiAwareMarkDuplicatesWithMateCigar-Picard-EXPERIMENTAL 2025-04-14T14:19:49Z https://gatk.broadinstitute.org/hc/en-us/articles/35967650118939-TransferReadTags-EXPERIMENTAL 2025-04-14T14:19:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967650255771-PossibleDeNovo 2025-04-14T14:19:51Z https://gatk.broadinstitute.org/hc/en-us/articles/35967650492059-BaseQualityRankSumTest 2025-04-14T14:19:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967650663195-ApplyVQSR 2025-04-14T14:19:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967651109019-CallCopyRatioSegments 2025-04-14T14:19:56Z https://gatk.broadinstitute.org/hc/en-us/articles/35967651193371-ScatterIntervalsByNs-Picard 2025-04-14T14:19:56Z https://gatk.broadinstitute.org/hc/en-us/articles/35967651997979-VcfFormatConverter-Picard 2025-04-14T14:20:00Z https://gatk.broadinstitute.org/hc/en-us/articles/35967652119195-PlotModeledSegments 2025-04-14T14:20:01Z https://gatk.broadinstitute.org/hc/en-us/articles/35967653366299-CalculateGenotypePosteriors 2025-04-14T14:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/35967654178075-CpcgMetrics 2025-04-14T14:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/35967654651931-FlagStat 2025-04-14T14:20:14Z https://gatk.broadinstitute.org/hc/en-us/articles/35967655401627-PrintVariantsSpark 2025-04-14T14:20:17Z https://gatk.broadinstitute.org/hc/en-us/articles/35967655474715-ValidateSamFile-Picard 2025-04-14T14:20:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967655634459-BpmToNormalizationManifestCsv-Picard 2025-04-14T14:20:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967655747227-FastqToSam-Picard 2025-04-14T14:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967656213403-ConvertHeaderlessHadoopBamShardToBam-BETA 2025-04-14T14:20:21Z https://gatk.broadinstitute.org/hc/en-us/articles/35967656433947-GatherVcfsCloud 2025-04-14T14:20:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967656762267-PassesVendorQualityCheckReadFilter 2025-04-14T14:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967657062683-SeqIsStoredReadFilter 2025-04-14T14:20:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967657207067-NonZeroReferenceLengthAlignmentReadFilter 2025-04-14T14:20:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967658252315-UnmarkDuplicates 2025-04-14T14:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967658394907-TargetedPcrMetrics 2025-04-14T14:20:07Z https://gatk.broadinstitute.org/hc/en-us/articles/35967658707227-SVStratify-BETA 2025-04-14T14:20:08Z https://gatk.broadinstitute.org/hc/en-us/articles/35967659188891-ExtractSVEvidenceSpark-BETA 2025-04-14T14:20:11Z https://gatk.broadinstitute.org/hc/en-us/articles/35967659272987-CollectAllelicCounts 2025-04-14T14:20:11Z https://gatk.broadinstitute.org/hc/en-us/articles/35967659563547-FingerprintingSummaryMetrics 2025-04-14T14:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/35967659638811-PreprocessIntervals 2025-04-14T14:20:13Z https://gatk.broadinstitute.org/hc/en-us/articles/35967659946395-GroupedSVCluster-BETA 2025-04-14T14:20:14Z https://gatk.broadinstitute.org/hc/en-us/articles/35967660325915-GtfToBed 2025-04-14T14:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/35967661113627-WgsMetrics 2025-04-14T14:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967661254171-SortSam-Picard 2025-04-14T14:20:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967662497179-RampedHaplotypeCaller-EXPERIMENTAL 2025-04-14T14:20:26Z https://gatk.broadinstitute.org/hc/en-us/articles/35967662766235-VariantRecalibrator 2025-04-14T14:20:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967664077083-DepthOfCoverage-BETA 2025-04-14T14:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967664211611-BaseErrorMetric 2025-04-14T14:20:34Z https://gatk.broadinstitute.org/hc/en-us/articles/35967664589467-SplitSamByLibrary-Picard 2025-04-14T14:20:36Z https://gatk.broadinstitute.org/hc/en-us/articles/35967664697499-CrosscheckFingerprints-Picard 2025-04-14T14:20:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967664819099-TandemRepeat 2025-04-14T14:20:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967665028635-AnalyzeSaturationMutagenesis-BETA 2025-04-14T14:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967665202331-Concordance 2025-04-14T14:20:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967665264027-FragmentLengthReadFilter 2025-04-14T14:20:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967666197787-FastaReferenceMaker 2025-04-14T14:20:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967666753691-RevertOriginalBaseQualitiesAndAddMateCigar-Picard 2025-04-14T14:20:11Z https://gatk.broadinstitute.org/hc/en-us/articles/35967666912539-MethylationTypeCaller-EXPERIMENTAL 2025-04-14T14:20:12Z https://gatk.broadinstitute.org/hc/en-us/articles/35967667589403-IlluminaPhasingMetrics 2025-04-14T14:20:15Z https://gatk.broadinstitute.org/hc/en-us/articles/35967668637211-SamToFastq-Picard 2025-04-14T14:20:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967669381147-PathSeqScoreSpark 2025-04-14T14:20:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967669788699-BaseQuality 2025-04-14T14:20:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967669941403-IntervalOverlapReadFilter 2025-04-14T14:20:25Z https://gatk.broadinstitute.org/hc/en-us/articles/35967670154395-GroundTruthReadsBuilder-EXPERIMENTAL 2025-04-14T14:20:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967670462747-ExtractOriginalAlignmentRecordsByNameSpark-BETA 2025-04-14T14:20:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967671013531-CycleSkipStatus 2025-04-14T14:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967671142171-HmerIndelNuc 2025-04-14T14:20:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967671200027-StructuralVariationDiscoveryPipelineSpark-BETA 2025-04-14T14:20:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967671919387-ProperlyPairedReadFilter 2025-04-14T14:20:34Z https://gatk.broadinstitute.org/hc/en-us/articles/35967672560795-AddCommentsToBam-Picard 2025-04-14T14:20:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967674195483-ConvertSequencingArtifactToOxoG-Picard 2025-04-14T14:20:46Z https://gatk.broadinstitute.org/hc/en-us/articles/35967674387355-CountNs 2025-04-14T14:20:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967675697307-AS-MappingQualityRankSumTest 2025-04-14T14:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967675740955-ReadPosRankSumTest 2025-04-14T14:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967676335131-PathSeqFilterSpark 2025-04-14T14:20:28Z https://gatk.broadinstitute.org/hc/en-us/articles/35967676533275-SVConcordance-BETA 2025-04-14T14:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967676724251-SplitIntervals 2025-04-14T14:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967678017563-FilterFuncotations-EXPERIMENTAL 2025-04-14T14:20:36Z https://gatk.broadinstitute.org/hc/en-us/articles/35967678260379-GenotypeGVCFs 2025-04-14T14:20:37Z https://gatk.broadinstitute.org/hc/en-us/articles/35967678371355-FindBadGenomicKmersSpark-BETA 2025-04-14T14:20:38Z https://gatk.broadinstitute.org/hc/en-us/articles/35967678625563-AS-BaseQualityRankSumTest 2025-04-14T14:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967679015707-FindMendelianViolations-Picard 2025-04-14T14:20:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967679085339-WgsMetricsWithNonZeroCoverage 2025-04-14T14:20:42Z https://gatk.broadinstitute.org/hc/en-us/articles/35967679408283-IndexFeatureFile 2025-04-14T14:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967679534491-ValidAlignmentEndReadFilter 2025-04-14T14:20:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967679813915-DepthPerSampleHC 2025-04-14T14:20:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967680151579-OrientationBiasReadCounts 2025-04-14T14:20:46Z https://gatk.broadinstitute.org/hc/en-us/articles/35967681327259-CalibrateDragstrModel 2025-04-14T14:20:51Z https://gatk.broadinstitute.org/hc/en-us/articles/35967681710235-GtcToVcf-Picard 2025-04-14T14:20:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967681930011-CheckTerminatorBlock-Picard 2025-04-14T14:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967682036891-CleanSam-Picard 2025-04-14T14:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967684051611-CombineGenotypingArrayVcfs-Picard 2025-04-14T14:20:15Z https://gatk.broadinstitute.org/hc/en-us/articles/35967684396571-ReadLengthEqualsCigarLengthReadFilter 2025-04-14T14:20:16Z https://gatk.broadinstitute.org/hc/en-us/articles/35967684728347-FlowBasedTPAttributeValidReadFilter 2025-04-14T14:20:18Z https://gatk.broadinstitute.org/hc/en-us/articles/35967684864283-IndependentReplicateMetric 2025-04-14T14:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967685172891-GcBiasDetailMetrics 2025-04-14T14:20:20Z https://gatk.broadinstitute.org/hc/en-us/articles/35967685432091-MergeSamFiles-Picard 2025-04-14T14:20:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967685955867-SplitReads 2025-04-14T14:20:24Z https://gatk.broadinstitute.org/hc/en-us/articles/35967686574107-CollectBaseDistributionByCycleSpark-BETA 2025-04-14T14:20:27Z https://gatk.broadinstitute.org/hc/en-us/articles/35967687568795-EvaluateInfoFieldConcordance-BETA 2025-04-14T14:20:31Z https://gatk.broadinstitute.org/hc/en-us/articles/35967687751195-NonZeroFragmentLengthReadFilter 2025-04-14T14:20:32Z https://gatk.broadinstitute.org/hc/en-us/articles/35967689238939-BuildBamIndex-Picard 2025-04-14T14:20:40Z https://gatk.broadinstitute.org/hc/en-us/articles/35967689350299-NotSecondaryAlignmentReadFilter 2025-04-14T14:20:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967689713179-ShiftFasta-BETA 2025-04-14T14:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967691008411-CollectOxoGMetrics-Picard 2025-04-14T14:20:49Z https://gatk.broadinstitute.org/hc/en-us/articles/35967691255451-CountReadsSpark 2025-04-14T14:20:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967691814555-FilterVariantTranches 2025-04-14T14:20:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967692284443-JointGermlineCNVSegmentation-BETA 2025-04-14T14:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967692611739-CigarContainsNoNOperator 2025-04-14T14:20:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967692671131-SplitVcfs-Picard 2025-04-14T14:20:35Z https://gatk.broadinstitute.org/hc/en-us/articles/35967693714971-CollectRrbsMetrics-Picard 2025-04-14T14:20:41Z https://gatk.broadinstitute.org/hc/en-us/articles/35967694344091-MetricsReadFilter 2025-04-14T14:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967694472475-FingerprintingDetailMetrics 2025-04-14T14:20:44Z https://gatk.broadinstitute.org/hc/en-us/articles/35967695018011-AssemblyComplexity 2025-04-14T14:20:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967695206043-RenameSampleInVcf-Picard 2025-04-14T14:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967695261851-ReadAnonymizer-EXPERIMENTAL 2025-04-14T14:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967695341595-MappingQualityAvailableReadFilter 2025-04-14T14:20:48Z https://gatk.broadinstitute.org/hc/en-us/articles/35967695506075-CreateReadCountPanelOfNormals 2025-04-14T14:20:49Z https://gatk.broadinstitute.org/hc/en-us/articles/35967696160155-CallableLoci-EXPERIMENTAL 2025-04-14T14:20:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967700642843-ReadGroupBlackListReadFilter 2025-04-14T14:20:19Z https://gatk.broadinstitute.org/hc/en-us/articles/35967701025563-CollectIlluminaBasecallingMetrics-Picard 2025-04-14T14:20:21Z https://gatk.broadinstitute.org/hc/en-us/articles/35967701323163-CollectRnaSeqMetrics-Picard 2025-04-14T14:20:22Z https://gatk.broadinstitute.org/hc/en-us/articles/35967701459355-AnnotateIntervals 2025-04-14T14:20:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967701568155-RevertSam-Picard 2025-04-14T14:20:23Z https://gatk.broadinstitute.org/hc/en-us/articles/35967702783899-PlotDenoisedCopyRatios 2025-04-14T14:20:29Z https://gatk.broadinstitute.org/hc/en-us/articles/35967703029147-FastaAlternateReferenceMaker 2025-04-14T14:20:30Z https://gatk.broadinstitute.org/hc/en-us/articles/35967703515931-SplitNCigarReads 2025-04-14T14:20:32Z https://gatk.broadinstitute.org/hc/en-us/articles/35967703905691-PileupSpark-BETA 2025-04-14T14:20:33Z https://gatk.broadinstitute.org/hc/en-us/articles/35967704760219-AS-QualByDepth 2025-04-14T14:20:39Z https://gatk.broadinstitute.org/hc/en-us/articles/35967705411739-IndelErrorMetric 2025-04-14T14:20:42Z https://gatk.broadinstitute.org/hc/en-us/articles/35967705623195-ReferenceBases 2025-04-14T14:20:43Z https://gatk.broadinstitute.org/hc/en-us/articles/35967706081179-QualityScoreDistributionSpark-BETA 2025-04-14T14:20:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967706266267-AlleleFraction 2025-04-14T14:20:45Z https://gatk.broadinstitute.org/hc/en-us/articles/35967707936027-CreateSomaticPanelOfNormals-BETA 2025-04-14T14:20:52Z https://gatk.broadinstitute.org/hc/en-us/articles/35967708025371-CheckPileup 2025-04-14T14:20:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967709463963-HmerMotifs 2025-04-14T14:20:53Z https://gatk.broadinstitute.org/hc/en-us/articles/35967717192731-InsertSizeMetrics 2025-04-14T14:20:47Z https://gatk.broadinstitute.org/hc/en-us/articles/35967717597979-CollectDuplicateMetrics-Picard 2025-04-14T14:20:49Z https://gatk.broadinstitute.org/hc/en-us/articles/35967717763995-CountBasesSpark 2025-04-14T14:20:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967717865499-PrintReadsSpark 2025-04-14T14:20:50Z https://gatk.broadinstitute.org/hc/en-us/articles/35967718017563-ASEReadCounter 2025-04-14T14:20:51Z https://gatk.broadinstitute.org/hc/en-us/articles/35967725741595-QualityYieldMetrics 2025-04-14T14:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/35967725880603-ReadLengthReadFilter 2025-04-14T14:20:54Z https://gatk.broadinstitute.org/hc/en-us/articles/41565974956955-Broad-and-Intel-accelerate-DRAGEN-GATK-HaplotypeCaller-on-Xeon-driving-3-fold-decrease-in-costs-and-making-CPUs-a-top-tier-platform-for-genomics 2025-09-29T17:32:37Z https://gatk.broadinstitute.org/hc/en-us/sections/360007134212-Computing-Platforms 2024-06-25T07:18:27Z https://gatk.broadinstitute.org/hc/en-us/sections/360007134392-Glossary 2026-03-30T12:25:26Z https://gatk.broadinstitute.org/hc/en-us/sections/360007134472-Events 2024-11-09T06:15:29Z https://gatk.broadinstitute.org/hc/en-us/sections/360007226611-FAQ 2026-02-06T14:55:06Z https://gatk.broadinstitute.org/hc/en-us/sections/360007226631-Tutorials 2026-02-06T20:35:24Z https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows 2025-05-27T13:06:18Z https://gatk.broadinstitute.org/hc/en-us/sections/360007226771-Algorithms 2025-03-28T14:44:20Z https://gatk.broadinstitute.org/hc/en-us/sections/360007226791-Troubleshooting-GATK4-Issues 2025-09-15T15:11:23Z https://gatk.broadinstitute.org/hc/en-us/sections/360007279452-4-1-4-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007279472-4-1-3-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007279512-4-1-1-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007279572-4-1-2-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007284952-4-0-8-1 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007286712-4-0-9-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007286812-4-0-5-2 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007286912-4-0-5-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007287472-4-0-11-0 2024-12-06T04:57:50Z https://gatk.broadinstitute.org/hc/en-us/sections/360007336992-4-0-1-1 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007337052-4-0-1-2 2025-12-19T20:12:43Z https://gatk.broadinstitute.org/hc/en-us/sections/360007337072-4-0-2-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007337472-4-0-4-0 2024-07-25T15:46:02Z https://gatk.broadinstitute.org/hc/en-us/sections/360007373191-Blog 2026-01-06T14:33:45Z https://gatk.broadinstitute.org/hc/en-us/sections/360007374491-4-1-0-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007379931-4-0-8-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007381251-4-0-7-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007381291-4-0-6-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007381571-4-0-5-1 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007382031-4-0-12-0 2024-09-15T13:59:00Z https://gatk.broadinstitute.org/hc/en-us/sections/360007382511-4-0-10-1 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007383151-4-0-10-0 2025-06-20T07:33:25Z https://gatk.broadinstitute.org/hc/en-us/sections/360007407371-4-0-1-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007407851-4-0-0-0 2025-03-22T01:35:03Z https://gatk.broadinstitute.org/hc/en-us/sections/360007430971-4-0-3-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360007458971-4-1-4-1 2025-07-01T14:55:26Z https://gatk.broadinstitute.org/hc/en-us/sections/360007720111-Forum-Bulletin 2026-02-10T04:14:48Z https://gatk.broadinstitute.org/hc/en-us/sections/360008011512-4-1-5-0 2024-12-16T16:20:00Z https://gatk.broadinstitute.org/hc/en-us/sections/360008481611-4-1-6-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360008763551-4-1-7-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360009656231-4-1-8-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360009803432-4-1-8-1 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360010932391-4-1-9-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/360012354372-4-2-0-0 2025-05-25T21:54:55Z https://gatk.broadinstitute.org/hc/en-us/sections/4404575821339-4-2-1-0 2025-04-08T23:01:31Z https://gatk.broadinstitute.org/hc/en-us/sections/4405443482011-4-2-2-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/4409917348379-4-2-3-0 2024-10-30T15:32:03Z https://gatk.broadinstitute.org/hc/en-us/sections/4413079114395-4-2-4-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/4414594300955-4-2-4-1 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/4418054201755-4-2-5-0 2025-03-06T08:26:27Z https://gatk.broadinstitute.org/hc/en-us/sections/5257848321819-4-2-6-0 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/5358821689883-4-2-6-1 2024-06-30T01:03:05Z https://gatk.broadinstitute.org/hc/en-us/sections/9570256638747-4-3-0-0 2025-09-30T15:51:08Z https://gatk.broadinstitute.org/hc/en-us/sections/13832625991067-4-4-0-0 2026-03-16T17:47:04Z https://gatk.broadinstitute.org/hc/en-us/sections/21904957852571-4-5-0-0 2025-11-03T18:48:56Z https://gatk.broadinstitute.org/hc/en-us/sections/27007892463131-4-6-0-0 2024-10-24T02:05:30Z https://gatk.broadinstitute.org/hc/en-us/sections/30331997704475-4-6-1-0-Current 2025-01-16T19:52:51Z https://gatk.broadinstitute.org/hc/en-us/sections/35967421676187-4-6-2-0 2025-04-14T14:20:54Z https://gatk.broadinstitute.org/hc/en-us/categories/360002302312-Getting-Started 2026-02-06T20:35:24Z https://gatk.broadinstitute.org/hc/en-us/categories/360002310591-Technical-Documentation 2026-03-30T12:25:26Z https://gatk.broadinstitute.org/hc/en-us/categories/360002310611-Announcements 2026-02-10T04:14:48Z https://gatk.broadinstitute.org/hc/en-us/categories/360002369672-Tool-Index 2026-03-16T17:47:04Z