4.0.6.0
Tool documentation for GATK release 4.0.6.0
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CompareBaseQualities
Compares the base qualities of two SAM/BAM/CRAM files Categ... -
CompareDuplicatesSpark (BETA)
Determine if two potentially identical BAMs have the same dupli... -
CompareMetrics (Picard)
Compare two metrics files.This tool compares the metrics and hi... -
CompareSAMs (Picard)
Compare two input ".sam" or ".bam" files. This tool initially ... -
Concordance (BETA)
Evaluate concordance of an input VCF against a validated truth ... -
ConvertHeaderlessHadoopBamShardToBam (BETA)
Convert a headerless BAM shard into a readable BAM Category... -
ConvertSequencingArtifactToOxoG (Picard)
Extract OxoG metrics from generalized artifacts metrics. This ... -
CountBases
Count bases in a SAM/BAM/CRAM file Category Coverage A... -
CountBasesInReference
Count the numbers of each base in a reference file Category... -
CountBasesSpark (BETA)
Counts bases in the input SAM/BAM Category Coverage An... -
CountFalsePositives (BETA)
Count PASS variants Category Variant Evaluation and Re... -
CountNs
Number of Ns at the pileup Category Variant Annotation... -
CountReads
Count reads in a SAM/BAM/CRAM file Category Coverage A... -
CountReadsSpark (BETA)
Counts reads in the input SAM/BAM Category Coverage An... -
CountVariants
Counts variant records in a VCF file, regardless of filter stat... -
CountVariantsSpark (BETA)
CountVariants on Spark Category Variant Evaluation and... -
Coverage
Total depth of coverage per sample and over all samples (DP) ... -
CpxVariantReInterpreterSpark (BETA)
(Internal) Tries to extract simple variants from a provided GAT... -
CreateHadoopBamSplittingIndex (BETA)
Create a Hadoop BAM splitting index Category Other ... -
CreateReadCountPanelOfNormals (BETA)
Creates a panel of normals for read-count denoising Categor... -
CreateSequenceDictionary (Picard)
Creates a sequence dictionary for a reference sequence. This t... -
CreateSomaticPanelOfNormals (BETA)
Make a panel of normals for use with Mutect2 Category ... -
CreateVerifyIDIntensityContaminationMetricsFile (Picard)
CreateVerifyIDIntensityContaminationMetricsFile takes an output... -
CrosscheckFingerprints (Picard)
Checks that all data in the set of input files appear to come f... -
CrosscheckReadGroupFingerprints (Picard)
DEPRECATED: USE CrosscheckFingerprints. Checks if all read grou... -
DenoiseReadCounts (BETA)
Denoises read counts to produce denoised copy ratios Catego... -
DepthPerAlleleBySample
Depth of coverage of each allele per sample (AD) Category ... -
DepthPerSampleHC
Depth of informative coverage for each sample (DP) Category... -
DetermineGermlineContigPloidy (BETA)
Determines the baseline contig ploidy for germline samples give... -
DiscoverVariantsFromContigAlignmentsSAMSpark (BETA)
(Internal) Examines aligned contigs from local assemblies and c...