4.0.2.0
Tool documentation for GATK release 4.0.2.0
-
FisherStrand
Strand bias estimated using Fisher's exact test (FS) Category ... -
FixCallSetSampleOrdering (EXPERIMENTAL)
fix sample names in a shuffled callset Category Other ... -
FixMateInformation (Picard)
Verify mate-pair information between mates and fix if needed.This tool ... -
FixMisencodedBaseQualityReads
Fix Illumina base quality scores in a SAM/BAM/CRAM file Category ... -
FixVcfHeader (Picard)
Replaces or fixes a VCF header.This tool will either replace the header... -
FlagStat
Accumulate flag statistics given a BAM file Category Diagnosti... -
FlagStatSpark (BETA)
Spark tool to accumulate flag statistics Category Diagnostics ... -
FragmentLength
Median fragment length of reads supporting each allele (MFRL) Categ... -
FragmentLengthReadFilter
Keep only read pairs with insert length less than or equal to the given... -
FuncotateSegments (BETA)
Functional annotation for segment files. The output formats are not we... -
Funcotator (BETA)
Functional Annotator Category Variant Evaluation and Refinemen... -
FuncotatorDataSourceDownloader (BETA)
Data source downloader for Funcotator. Category Variant Evalua... -
GatherBamFiles (Picard)
Concatenate efficiently BAM files that resulted from a scattered parall... -
GatherBQSRReports
Gathers scattered BQSR recalibration reports into a single file Cat... -
GatherTranches (BETA)
Gathers scattered VQSLOD tranches into a single file Category ... -
GatherVcfs (Picard)
Gathers multiple VCF files from a scatter operation into a single VCF f... -
GatherVcfsCloud (BETA)
Gathers multiple VCF files from a scatter operation into a single VCF f... -
GenomicsDBImport
Import VCFs to GenomicsDB Category Short Variant Discovery ... -
GenotypeConcordance (Picard)
Calculates the concordance between genotype data of one samples in each... -
GenotypeGVCFs
Perform joint genotyping on one or more samples pre-called with Haploty... -
GenotypeSummaries
Summary of genotype statistics from all samples (NCC, GQ_MEAN, GQ_STDDE... -
GermlineCNVCaller (BETA)
Calls copy-number variants in germline samples given their counts and t... -
GetPileupSummaries (BETA)
Tabulates pileup metrics for inferring contamination Category ... -
GetSampleName (BETA)
Emit a single sample name Category Diagnostics and Quality Con... -
GnarlyGenotyper (BETA)
Perform "quick and dirty" joint genotyping on one or more samples pre-c... -
GoodCigarReadFilter
Keep only reads containing good CIGAR string Category Read Fil... -
GtcToVcf (Picard)
GtcToVcf takes an Illumina GTC file and converts it to a VCF file using... -
HaplotypeCaller
Call germline SNPs and indels via local re-assembly of haplotypes C... -
HaplotypeCallerSpark (BETA)
HaplotypeCaller on Spark Category Short Variant Discovery ... -
HasReadGroupReadFilter
Filter out reads without Read Group Category Read Filters ...