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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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  3. 4.0.1.0

4.0.1.0

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Tool documentation for GATK release 4.0.1.0

  • * Tool Documentation Index
    Copy Number Variant Discovery Tools that analyze read coverage to detec...
  • AccumulateVariantCallingMetrics (Picard)
    Combines multiple Variant Calling Metrics files into a single file. Th...
  • AddCommentsToBam (Picard)
    Adds comments to the header of a BAM file.This tool makes a copy of the...
  • AddOATag (Picard)
    This tool takes in an aligned SAM or BAM and adds the OA tag to every a...
  • AddOrReplaceReadGroups (Picard)
    Assigns all the reads in a file to a single new read-group. This tool ...
  • AlignmentAgreesWithHeaderReadFilter
    Filters out reads where the alignment does not match the contents of th...
  • AlleleFraction
    Variant allele fraction for a genotype Category Variant Annota...
  • AllowAllReadsReadFilter
    Do not filter out any read Category Read Filters Over...
  • AmbiguousBaseReadFilter
    Filters out reads that have greater than the threshold number of N base...
  • AnalyzeCovariates
    Evaluate and compare base quality score recalibration (BQSR) tables ...
  • AnalyzeSaturationMutagenesis (BETA)
    (EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutag...
  • AnnotateIntervals (BETA)
    Annotates intervals with GC content Category Copy Number Varia...
  • AnnotatePairOrientation (BETA)
    (EXPERIMENTAL) Annotate a non-M2 VCF (using the associated tumor bam) w...
  • AnnotateVcfWithBamDepth
    (Internal) Annotate a vcf with a bam's read depth at each variant locus...
  • AnnotateVcfWithExpectedAlleleFraction
    (Internal) Annotate a vcf with expected allele fractions in pooled sequ...
  • ApplyBQSR
    Apply base quality score recalibration Category Read Data Mani...
  • ApplyBQSRSpark (BETA)
    Apply base quality score recalibration on Spark Category Read ...
  • ApplyVQSR
    Apply a score cutoff to filter variants based on a recalibration table...
  • ASEReadCounter
    Generates table of filtered base counts at het sites for allele specifi...
  • AS_BaseQualityRankSumTest
    Allele-specific rank sum test of REF versus ALT base quality scores (AS...
  • AS_FisherStrand
    Allele-specific strand bias estimated using Fisher's exact test (AS_FS)...
  • AS_InbreedingCoeff
    Allele-specific likelihood-based test for the consanguinity among sampl...
  • AS_MappingQualityRankSumTest
    Allele-specific rank sum test for mapping qualities of REF versus ALT r...
  • AS_QualByDepth
    Allele-specific call confidence normalized by depth of sample reads sup...
  • AS_ReadPosRankSumTest
    Allele-specific rank sum test for relative positioning of REF versus AL...
  • AS_RMSMappingQuality
    Allele-specific root-mean-square of the mapping quality of reads across...
  • AS_StrandOddsRatio
    Allele-specific strand bias estimated by the symmetric odds ratio test ...
  • BaitDesigner (Picard)
    Designs oligonucleotide baits for hybrid selection reactions.This tool ...
  • BamIndexStats (Picard)
    Generate index statistics from a BAM fileThis tool calculates statistic...
  • BamToBfq (Picard)
    Converts a BAM file into a BFQ (binary fastq formatted) file.The BFQ fo...
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