4.0.1.0
Tool documentation for GATK release 4.0.1.0
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CombineGVCFs
Merges one or more HaplotypeCaller GVCF files into a single GVCF with a... -
CombineSegmentBreakpoints (EXPERIMENTAL)
Combine the breakpoints of two segment files and annotate the resulting... -
CompareBaseQualities
Compares the base qualities of two SAM/BAM/CRAM files Category ... -
CompareDuplicatesSpark (BETA)
Determine if two potentially identical BAMs have the same duplicate rea... -
CompareMetrics (Picard)
Compare two metrics files.This tool compares the metrics and histograms... -
CompareSAMs (Picard)
Compare two input ".sam" or ".bam" files. This tool initially compares... -
Concordance (BETA)
Evaluate concordance of an input VCF against a validated truth VCF ... -
ConvertHeaderlessHadoopBamShardToBam (BETA)
Convert a headerless BAM shard into a readable BAM Category Re... -
ConvertSequencingArtifactToOxoG (Picard)
Extract OxoG metrics from generalized artifacts metrics. This tool ext... -
CountBases
Count bases in a SAM/BAM/CRAM file Category Coverage Analysis ... -
CountBasesInReference
Count the numbers of each base in a reference file Category Re... -
CountBasesSpark (BETA)
Counts bases in the input SAM/BAM Category Coverage Analysis ... -
CountFalsePositives (BETA)
Count PASS variants Category Variant Evaluation and Refinement... -
CountNs
Number of Ns at the pileup Category Variant Annotations ... -
CountReads
Count reads in a SAM/BAM/CRAM file Category Coverage Analysis ... -
CountReadsSpark (BETA)
Counts reads in the input SAM/BAM Category Coverage Analysis ... -
CountVariants
Counts variant records in a VCF file, regardless of filter status. ... -
CountVariantsSpark (BETA)
CountVariants on Spark Category Variant Evaluation and Refinem... -
Coverage
Total depth of coverage per sample and over all samples (DP) Catego... -
CpxVariantReInterpreterSpark (BETA)
(Internal) Tries to extract simple variants from a provided GATK-SV CPX... -
CreateHadoopBamSplittingIndex (BETA)
Create a Hadoop BAM splitting index Category Other Ov... -
CreateReadCountPanelOfNormals (BETA)
Creates a panel of normals for read-count denoising Category C... -
CreateSequenceDictionary (Picard)
Creates a sequence dictionary for a reference sequence. This tool crea... -
CreateSomaticPanelOfNormals (BETA)
Make a panel of normals for use with Mutect2 Category Variant ... -
CreateVerifyIDIntensityContaminationMetricsFile (Picard)
CreateVerifyIDIntensityContaminationMetricsFile takes an output file as... -
CrosscheckFingerprints (Picard)
Checks that all data in the set of input files appear to come from the ... -
CrosscheckReadGroupFingerprints (Picard)
DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups withi... -
DenoiseReadCounts (BETA)
Denoises read counts to produce denoised copy ratios Category ... -
DepthPerAlleleBySample
Depth of coverage of each allele per sample (AD) Category Vari... -
DepthPerSampleHC
Depth of informative coverage for each sample (DP) Category Va...