4.2.4.0
Tool documentation for GATK release 4.2.4.0
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CollectVariantCallingMetrics (Picard)
Collects per-sample and aggregate (spanning all samples) metric... -
CollectWgsMetrics (Picard)
Collect metrics about coverage and performance of whole genome ... -
CollectWgsMetricsWithNonZeroCoverage (Picard) (EXPERIMENTAL)
Collect metrics about coverage and performance of whole genome ... -
CombineGenotypingArrayVcfs (Picard)
CombineGenotypingArrayVcfs takes one or more VCF files, as gene... -
CombineGVCFs
Merges one or more HaplotypeCaller GVCF files into a single GVC... -
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 ... -
ComposeSTRTableFile
Composes a genome-wide STR location table used for DragSTR mode... -
Concordance
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
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
Counts reads in the input SAM/BAM Category Coverage An... -
CountVariants
Counts variant records in a VCF file, regardless of filter stat... -
CountVariantsSpark
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... -
CreateBafRegressMetricsFile (Picard)
CreateBafRegressMetricsFile takes an output file as generated b... -
CreateHadoopBamSplittingIndex (BETA)
Create a Hadoop BAM splitting index Category Other ... -
CreateReadCountPanelOfNormals
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...