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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. 4.2.4.0

4.2.4.0

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Tool documentation for GATK release 4.2.4.0

  • HaplotypeCallerSpark (BETA)
    HaplotypeCaller on Spark Category Short Variant Discov...
  • HasReadGroupReadFilter
    Filter out reads without Read Group Category Read Filt...
  • IlluminaBasecallsToFastq (Picard)
    Generate FASTQ file(s) from Illumina basecall read data. This ...
  • IlluminaBasecallsToSam (Picard)
    Transforms raw Illumina sequencing data into an unmapped SAM or...
  • InbreedingCoeff
    Likelihood-based test for the consanguinity among samples (Inbr...
  • IndexFeatureFile
    Creates an index for a feature file, e.g. VCF or BED file. ...
  • IntervalListToBed (Picard)
    Converts an Picard IntervalList file to a BED file. Categor...
  • IntervalListTools (Picard)
    A tool for performing various IntervalList manipulations Summar...
  • IntervalOverlapReadFilter
    Filters out reads that don't overlap the specified region. NOTE...
  • LearnReadOrientationModel
    Get the maximum likelihood estimates of artifact prior probabil...
  • LeftAlignAndTrimVariants
    Left align and trim vairants Category Variant Manipula...
  • LeftAlignIndels
    Left-aligns indels from reads in a SAM/BAM/CRAM file Catego...
  • LibraryReadFilter
    Keep only reads from the specified library Category Re...
  • LiftOverIntervalList (Picard)
    Lifts over an interval list from one reference build to another...
  • LiftoverVcf (Picard)
    Lifts over a VCF file from one reference build to another. Sum...
  • LikelihoodRankSumTest
    Rank sum test of per-read likelihoods of REF versus ALT reads (...
  • LocalAssembler (BETA)
    Local assembler for SVs Category Coverage Analysis ...
  • MakeSitesOnlyVcf (Picard)
    This tool reads a VCF/VCF.gz/BCF and removes all genotype infor...
  • MappedReadFilter
    Filter out unmapped reads Category Read Filters ...
  • MappingQuality
    Median mapping quality of reads supporting each allele (MMQ) ...
  • MappingQualityAvailableReadFilter
    Filter out reads without available mapping quality Category...
  • MappingQualityNotZeroReadFilter
    Filter out reads with mapping quality equal to zero Categor...
  • MappingQualityRankSumTest
    Rank sum test for mapping qualities of REF versus ALT reads (MQ...
  • MappingQualityReadFilter
    Keep only reads with mapping qualities within a specified range...
  • MappingQualityZero
    Count of all reads with MAPQ = 0 across all samples (MQ0) C...
  • MarkDuplicates (Picard)
    Identifies duplicate reads. This tool locates and tags duplica...
  • MarkDuplicatesSpark
    MarkDuplicates on Spark Category Read Data Manipulatio...
  • MarkDuplicatesWithMateCigar (Picard)
    Identifies duplicate reads, accounting for mate CIGAR. This to...
  • MarkIlluminaAdapters (Picard)
    Reads a SAM or BAM file and rewrites it with new adapter-trimmi...
  • MatchingBasesAndQualsReadFilter
    Filter out reads where the bases and qualities do not match ...
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