4.0.6.0
Tool documentation for GATK release 4.0.6.0
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DownsampleSam (Picard)
Downsample a SAM or BAM file.This tool applies a downsampling a... -
EstimateLibraryComplexity (Picard)
Estimates the numbers of unique molecules in a sequencing libra... -
EstimateLibraryComplexityGATK (BETA)
Estimate library complexity from the sequence of read pairs ... -
EvaluateInfoFieldConcordance (BETA)
Evaluate concordance of info fields in an input VCF against a v... -
ExcessHet
Phred-scaled p-value for exact test of excess heterozygosity (E... -
ExtractIlluminaBarcodes (Picard)
Tool determines the barcode for each read in an Illumina lane. ... -
ExtractOriginalAlignmentRecordsByNameSpark (BETA)
Subsets reads by name Category Read Data Manipulation ... -
ExtractSequences (Picard)
Subsets intervals from a reference sequence to a new FASTA file... -
ExtractSVEvidenceSpark (BETA)
(Internal) Extracts evidence of structural variations from read... -
FastaAlternateReferenceMaker
Create an alternative reference by combining a fasta with a vcf... -
FastaReferenceMaker
Create snippets of a fasta file Category Reference ... -
FastqToSam (Picard)
Converts a FASTQ file to an unaligned BAM or SAM file.Output re... -
FifoBuffer (Picard)
Acts as a large memory buffer between processes that are connec... -
FilterAlignmentArtifacts (EXPERIMENTAL)
Filter alignment artifacts from a vcf callset. Category ... -
FilterByOrientationBias (EXPERIMENTAL)
Filter Mutect2 somatic variant calls using orientation bias ... -
FilterFuncotations (EXPERIMENTAL)
Filter variants based on clinically-significant Funcotations. ... -
FilterIntervals
Filters intervals based on annotations and/or count statistics ... -
FilterMutectCalls
Filter somatic SNVs and indels called by Mutect2 Category ... -
FilterMutectCalls
Filter somatic SNVs and indels called by Mutect2 Category ... -
FilterSamReads (Picard)
Subsets reads from a SAM or BAM file by applying one of several... -
FilterVariantTranches (EXPERIMENTAL)
Apply tranche filtering Category Variant Filtering ... -
FilterVcf (Picard)
Applies one or more hard filters to a VCF file to filter out ge... -
FindBadGenomicKmersSpark (BETA)
Identifies sequences that occur at high frequency in a referenc... -
FindBreakpointEvidenceSpark (BETA)
(Internal) Produces local assemblies of genomic regions that ma... -
FindMendelianViolations (Picard)
Takes in VCF or BCF and a pedigree file and looks for high conf... -
FirstOfPairReadFilter
Keep only reads that are first of pair Category Read F... -
FisherStrand
Strand bias estimated using Fisher's exact test (FS) Catego... -
FixCallSetSampleOrdering (EXPERIMENTAL)
fix sample names in a shuffled callset Category Other ... -
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...