4.2.3.0
Tool documentation for GATK release 4.2.3.0
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FirstOfPairReadFilter
Keep only reads that are first of pair Category Read F... -
FisherStrand
Strand bias estimated using Fisher's exact test (FS) Catego... -
FixMateInformation (Picard)
Verify mate-pair information between mates and fix if needed.Th... -
FixMisencodedBaseQualityReads
Fix Illumina base quality scores in a SAM/BAM/CRAM file Cat... -
FixVcfHeader (Picard)
Replaces or fixes a VCF header.This tool will either replace th... -
FlagStat
Accumulate flag statistics given a BAM file Category D... -
FlagStatSpark
Spark tool to accumulate flag statistics Category Diag... -
FragmentDepthPerAlleleBySample
Depth of coverage of each allele per sample (AD) Category ... -
FragmentLength
Median fragment length of reads supporting each allele (MFRL) ... -
FragmentLengthReadFilter
Keep only read pairs with insert length less than or equal to t... -
FuncotateSegments (BETA)
Functional annotation for segment files. The output formats ar... -
Funcotator
Functional Annotator Category Variant Evaluation and R... -
FuncotatorDataSourceDownloader
Data source downloader for Funcotator. Category Varian... -
GatherBamFiles (Picard)
Concatenate efficiently BAM files that resulted from a scattere... -
GatherBQSRReports
Gathers scattered BQSR recalibration reports into a single file... -
GatherTranches (BETA)
Gathers scattered VQSLOD tranches into a single file Catego... -
GatherVcfs (Picard)
Gathers multiple VCF files from a scatter operation into a sing... -
GatherVcfsCloud (BETA)
Gathers multiple VCF files from a scatter operation into a sing... -
GeneExpressionEvaluation (BETA)
Evaluate gene expression from RNA-seq reads aligned to genome. ... -
GenomicsDBImport
Import VCFs to GenomicsDB Category Short Variant Disco... -
GenotypeConcordance (Picard)
Calculates the concordance between genotype data of one sample ... -
GenotypeGVCFs
Perform joint genotyping on one or more samples pre-called with... -
GenotypeSummaries
Summary of genotype statistics from all samples (NCC, GQ_MEAN, ... -
GermlineCNVCaller
Calls copy-number variants in germline samples given their coun... -
GetPileupSummaries
Tabulates pileup metrics for inferring contamination Catego... -
GetSampleName
Emit a single sample name Category Diagnostics and Qua... -
GnarlyGenotyper (BETA)
Perform "quick and dirty" joint genotyping on one or more sampl... -
GoodCigarReadFilter
Keep only reads containing good CIGAR string Category ... -
GtcToVcf (Picard)
GtcToVcf takes an Illumina GTC file and converts it to a VCF fi... -
HaplotypeCaller
Call germline SNPs and indels via local re-assembly of haplotyp...