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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. 4.1.4.1

4.1.4.1

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Tool documentation for GATK release 4.1.4.1

  • * Tool Documentation Index
    Copy Number Variant Discovery Tools that analyze read coverage to d...
  • AccumulateVariantCallingMetrics (Picard)
    Combines multiple Variant Calling Metrics files into a single f...
  • AddCommentsToBam (Picard)
    Adds comments to the header of a BAM file.This tool makes a cop...
  • AddOATag (Picard)
    This tool takes in an aligned SAM or BAM and adds the OA tag to...
  • AddOrReplaceReadGroups (Picard)
    Assigns all the reads in a file to a single new read-group. Th...
  • AlignmentAgreesWithHeaderReadFilter
    Filters out reads where the alignment does not match the conten...
  • AlleleFraction
    Variant allele fraction for a genotype Category Varian...
  • AlleleFrequency
    Stratify by eval RODs by the allele frequency of the alternate...
  • AllowAllReadsReadFilter
    Do not filter out any read Category Read Filters ...
  • AmbiguousBaseReadFilter
    Filters out reads that have greater than the threshold number o...
  • AnalyzeCovariates
    Evaluate and compare base quality score recalibration (BQSR) ta...
  • AnalyzeSaturationMutagenesis (BETA)
    (EXPERIMENTAL) Processes reads from a MITESeq or other saturati...
  • AnnotateIntervals
    Annotates intervals with GC content, mappability, and segmental...
  • AnnotatePairOrientation (EXPERIMENTAL)
    Annotate a non-M2 VCF (using the associated tumor bam) with pai...
  • AnnotateVcfWithBamDepth
    (Internal) Annotate a vcf with a bam's read depth at each varia...
  • AnnotateVcfWithExpectedAlleleFraction
    (Internal) Annotate a vcf with expected allele fractions in poo...
  • ApplyBQSR
    Apply base quality score recalibration Category Read D...
  • ApplyBQSRSpark (BETA)
    Apply base quality score recalibration on Spark Category ...
  • ApplyVQSR
    Apply a score cutoff to filter variants based on a recalibrati...
  • ASEReadCounter
    Generates table of filtered base counts at het sites for allele...
  • AS_BaseQualityRankSumTest
    Allele-specific rank sum test of REF versus ALT base quality sc...
  • AS_FisherStrand
    Allele-specific strand bias estimated using Fisher's exact test...
  • AS_InbreedingCoeff
    Allele-specific likelihood-based test for the consanguinity amo...
  • AS_MappingQualityRankSumTest
    Collects fragment counts at specified intervals Category Cover...
  • AS_MappingQualityRankSumTest
    Allele-specific rank sum test for mapping qualities of REF vers...
  • AS_QualByDepth
    Allele-specific call confidence normalized by depth of sample r...
  • AS_ReadPosRankSumTest
    Allele-specific rank sum test for relative positioning of REF v...
  • AS_RMSMappingQuality
    Allele-specific root-mean-square of the mapping quality of read...
  • AS_StrandOddsRatio
    Allele-specific strand bias estimated by the symmetric odds rat...
  • BaitDesigner (Picard)
    Designs oligonucleotide baits for hybrid selection reactions.Th...
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