4.0.1.0
Tool documentation for GATK release 4.0.1.0
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DetermineGermlineContigPloidy (BETA)
Determines the baseline contig ploidy for germline samples given counts... -
DiscoverVariantsFromContigAlignmentsSAMSpark (BETA)
(Internal) Examines aligned contigs from local assemblies and calls str... -
DownsampleSam (Picard)
Downsample a SAM or BAM file.This tool applies a downsampling algorithm... -
EstimateLibraryComplexity (Picard)
Estimates the numbers of unique molecules in a sequencing library. Thi... -
EstimateLibraryComplexityGATK (BETA)
Estimate library complexity from the sequence of read pairs Categor... -
EvaluateInfoFieldConcordance (BETA)
Evaluate concordance of info fields in an input VCF against a validated... -
ExcessHet
Phred-scaled p-value for exact test of excess heterozygosity (ExcessHet... -
ExtractIlluminaBarcodes (Picard)
Tool determines the barcode for each read in an Illumina lane. This to... -
ExtractOriginalAlignmentRecordsByNameSpark (BETA)
Subsets reads by name Category Read Data Manipulation ... -
ExtractSequences (Picard)
Subsets intervals from a reference sequence to a new FASTA file.This to... -
ExtractSVEvidenceSpark (BETA)
(Internal) Extracts evidence of structural variations from reads Ca... -
FastaAlternateReferenceMaker
Create an alternative reference by combining a fasta with a vcf. Ca... -
FastaReferenceMaker
Create snippets of a fasta file Category Reference Ov... -
FastqToSam (Picard)
Converts a FASTQ file to an unaligned BAM or SAM file.Output read recor... -
FifoBuffer (Picard)
Acts as a large memory buffer between processes that are connected with... -
FilterAlignmentArtifacts (EXPERIMENTAL)
Filter alignment artifacts from a vcf callset. Category Varian... -
FilterByOrientationBias (EXPERIMENTAL)
Filter Mutect2 somatic variant calls using orientation bias Categor... -
FilterFuncotations (EXPERIMENTAL)
Filter variants based on clinically-significant Funcotations. Categ... -
FilterIntervals (BETA)
Filters intervals based on annotations and/or count statistics Cate... -
FilterLongReadAlignmentsSAMSpark (EXPERIMENTAL)
Examines alignments of chimeric contigs, attempting to produce an optim... -
FilterMutectCalls
Filter somatic SNVs and indels called by Mutect2 Category Vari... -
FilterMutectCalls (BETA)
Filter somatic SNVs and indels called by Mutect2 Category Vari... -
FilterSamReads (Picard)
Subsets reads from a SAM or BAM file by applying one of several filters... -
FilterVariantTranches (EXPERIMENTAL)
Apply tranche filtering Category Variant Filtering Ov... -
FilterVcf (Picard)
Applies one or more hard filters to a VCF file to filter out genotypes ... -
FindBadGenomicKmersSpark (BETA)
Identifies sequences that occur at high frequency in a reference Ca... -
FindBreakpointEvidenceSpark (BETA)
(Internal) Produces local assemblies of genomic regions that may harbor... -
FindMendelianViolations (Picard)
Takes in VCF or BCF and a pedigree file and looks for high confidence c... -
FirstOfPairReadFilter
Keep only reads that are first of pair Category Read Filters ... -
FisherStrand
Strand bias estimated using Fisher's exact test (FS) Category ...