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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. 4.0.2.0

4.0.2.0

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Tool documentation for GATK release 4.0.2.0

  • FisherStrand
    Strand bias estimated using Fisher's exact test (FS) Category ...
  • FixCallSetSampleOrdering (EXPERIMENTAL)
    fix sample names in a shuffled callset Category Other ...
  • FixMateInformation (Picard)
    Verify mate-pair information between mates and fix if needed.This tool ...
  • FixMisencodedBaseQualityReads
    Fix Illumina base quality scores in a SAM/BAM/CRAM file Category ...
  • FixVcfHeader (Picard)
    Replaces or fixes a VCF header.This tool will either replace the header...
  • FlagStat
    Accumulate flag statistics given a BAM file Category Diagnosti...
  • FlagStatSpark (BETA)
    Spark tool to accumulate flag statistics Category Diagnostics ...
  • FragmentLength
    Median fragment length of reads supporting each allele (MFRL) Categ...
  • FragmentLengthReadFilter
    Keep only read pairs with insert length less than or equal to the given...
  • FuncotateSegments (BETA)
    Functional annotation for segment files. The output formats are not we...
  • Funcotator (BETA)
    Functional Annotator Category Variant Evaluation and Refinemen...
  • FuncotatorDataSourceDownloader (BETA)
    Data source downloader for Funcotator. Category Variant Evalua...
  • GatherBamFiles (Picard)
    Concatenate efficiently BAM files that resulted from a scattered parall...
  • GatherBQSRReports
    Gathers scattered BQSR recalibration reports into a single file Cat...
  • GatherTranches (BETA)
    Gathers scattered VQSLOD tranches into a single file Category ...
  • GatherVcfs (Picard)
    Gathers multiple VCF files from a scatter operation into a single VCF f...
  • GatherVcfsCloud (BETA)
    Gathers multiple VCF files from a scatter operation into a single VCF f...
  • GenomicsDBImport
    Import VCFs to GenomicsDB Category Short Variant Discovery ...
  • GenotypeConcordance (Picard)
    Calculates the concordance between genotype data of one samples in each...
  • GenotypeGVCFs
    Perform joint genotyping on one or more samples pre-called with Haploty...
  • GenotypeSummaries
    Summary of genotype statistics from all samples (NCC, GQ_MEAN, GQ_STDDE...
  • GermlineCNVCaller (BETA)
    Calls copy-number variants in germline samples given their counts and t...
  • GetPileupSummaries (BETA)
    Tabulates pileup metrics for inferring contamination Category ...
  • GetSampleName (BETA)
    Emit a single sample name Category Diagnostics and Quality Con...
  • GnarlyGenotyper (BETA)
    Perform "quick and dirty" joint genotyping on one or more samples pre-c...
  • GoodCigarReadFilter
    Keep only reads containing good CIGAR string Category Read Fil...
  • GtcToVcf (Picard)
    GtcToVcf takes an Illumina GTC file and converts it to a VCF file using...
  • HaplotypeCaller
    Call germline SNPs and indels via local re-assembly of haplotypes C...
  • HaplotypeCallerSpark (BETA)
    HaplotypeCaller on Spark Category Short Variant Discovery ...
  • HasReadGroupReadFilter
    Filter out reads without Read Group Category Read Filters ...
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