4.1.4.0
Tool documentation for GATK release 4.1.4.0
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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 (BETA)
Spark tool to accumulate flag statistics Category Diag... -
FragmentLength
Median fragment length of reads supporting each allele (MFRL) ... -
FragmentLengthReadFilter
Keep only read pairs with insert length less than or equal to t... -
Funcotator (BETA)
Functional Annotator Category Variant Evaluation and R... -
FuncotatorDataSourceDownloader (BETA)
Data source downloader for Funcotator. Category Varian... -
GatherBamFiles (Picard)
Calculate statistics on fingerprints, checking their viabilityT... -
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... -
GenomicsDBImport
Import VCFs to GenomicsDB Category Short Variant Disco... -
GenotypeConcordance (Picard)
Calculates the concordance between genotype data of one samples... -
GenotypeGVCFs
Perform joint genotyping on one or more samples pre-called with... -
GenotypeSummaries
Summary of genotype statistics from all samples (NCC, GQ_MEAN, ... -
GermlineCNVCaller (BETA)
Calls copy-number variants in germline samples given their coun... -
GetPileupSummaries (BETA)
Tabulates pileup metrics for inferring contamination Catego... -
GetSampleName (BETA)
Emit a single sample name Category Diagnostics and Qua... -
GoodCigarReadFilter
Keep only reads containing good CIGAR string Category ... -
HaplotypeCaller
Call germline SNPs and indels via local re-assembly of haplotyp... -
HaplotypeCallerSpark (BETA)
HaplotypeCaller on Spark Category Short Variant Discov... -
HasReadGroupReadFilter
Filter out reads without Read Group Category Read Filt... -
IlluminaBasecallsToFastq (Picard)
Generate FASTQ file(s) from Illumina basecall read data. This ... -
IlluminaBasecallsToSam (Picard)
Transforms raw Illumina sequencing data into an unmapped SAM or... -
InbreedingCoeff
Likelihood-based test for the consanguinity among samples (Inbr... -
IndexFeatureFile
Creates an index for a feature file, e.g. VCF or BED file. ...