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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

  1. GATK
  2. Tool Index
  3. 4.0.1.0

4.0.1.0

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Tool documentation for GATK release 4.0.1.0

  • 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 ...
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