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Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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  2. Tool Index
  3. 4.2.2.0

4.2.2.0

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Tool documentation for GATK release 4.2.2.0

  • CrosscheckFingerprints (Picard)
    Checks that all data in the set of input files appear to come f...
  • DenoiseReadCounts
    Denoises read counts to produce denoised copy ratios Catego...
  • DepthOfCoverage (BETA)
    Generate coverage summary information for reads data Catego...
  • DepthPerAlleleBySample
    Depth of coverage of each allele per sample (AD) Category ...
  • DepthPerSampleHC
    Depth of informative coverage for each sample (DP) Category...
  • DetermineGermlineContigPloidy
    Determines the baseline contig ploidy for germline samples give...
  • DiscoverVariantsFromContigAlignmentsSAMSpark (BETA)
    (Internal) Examines aligned contigs from local assemblies and c...
  • 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...
  • 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...
  • FeaturizedReadSets
    Featurized read sets for Mutect3 training data Category ...
  • FifoBuffer (Picard)
    Acts as a large memory buffer between processes that are connec...
  • FilterAlignmentArtifacts (EXPERIMENTAL)
    Filter alignment artifacts from a vcf callset. Category ...
  • 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 ...
  • FilterSamReads (Picard)
    Subsets reads from a SAM or BAM file by applying one of several...
  • FilterVariantTranches
    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...
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