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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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  2. Tool Index
  3. 4.0.5.2

4.0.5.2

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Tool documentation for GATK release 4.0.5.2

  • PlotDenoisedCopyRatios (BETA)
    Creates plots of denoised copy ratios Category Copy Nu...
  • PlotModeledSegments (BETA)
    Creates plots of denoised and segmented copy-ratio and minor-al...
  • PolymorphicNuMT
    Number of alts indicates it could be an autosomal false positiv...
  • PositionBasedDownsampleSam (Picard)
    Summary Class to downsample a SAM/BAM file based on the positio...
  • PossibleDeNovo
    Existence of a de novo mutation in at least one of the given fa...
  • PostprocessGermlineCNVCalls (BETA)
    Postprocesses the output of GermlineCNVCaller and generates VCF...
  • PreprocessIntervals (BETA)
    Prepares bins for coverage collection Category Interva...
  • PrimaryLineReadFilter
    Keep only reads representing primary alignments (those that sat...
  • PrintReads
    Print reads in the SAM/BAM/CRAM file Category Read Dat...
  • PrintReadsSpark (BETA)
    PrintReads on Spark Category Read Data Manipulation ...
  • PrintVariantsSpark (BETA)
    Prints out variants from the input VCF. Category Varia...
  • ProperlyPairedReadFilter
    Keep only reads that are properly paired Category Read...
  • QualByDepth
    Variant confidence normalized by unfiltered depth of variant sa...
  • QualityScoreDistribution (Picard)
    Chart the distribution of quality scores. This tool is used fo...
  • QualityScoreDistributionSpark (BETA)
    QualityScoreDistribution on Spark Category Diagnostics...
  • ReadGroupBlackListReadFilter
    Keep records not matching the read group tag and exact match st...
  • ReadGroupReadFilter
    Keep only reads from the specified read group Category ...
  • ReadLengthEqualsCigarLengthReadFilter
    Filter out reads where the read and CIGAR do not match in leng...
  • ReadLengthReadFilter
    Keep only reads whose length is within a certain range Cate...
  • ReadNameReadFilter
    Keep only reads with this read name Category Read Filt...
  • ReadPosition
    Median distance of variant starts from ends of reads supporting...
  • ReadPosRankSumTest
    Rank sum test for relative positioning of REF versus ALT allele...
  • ReadsPipelineSpark (BETA)
    Takes unaligned or aligned reads and runs BWA (if specified), M...
  • ReadStrandFilter
    Keep only reads whose strand is as specified Category ...
  • ReblockGVCF (EXPERIMENTAL)
    Condenses homRef blocks in a single-sample GVCF Category ...
  • ReferenceBases
    Annotate with local reference bases (REF_BASES) Category ...
  • RemoveNearbyIndels
    (Internal) Remove indels from the VCF file that are close to ea...
  • RenameSampleInVcf (Picard)
    This tool enables the user to rename a sample in either a VCF o...
  • ReorderSam (Picard)
    Not to be confused with SortSam which sorts a SAM or BAM file w...
  • ReplaceSamHeader (Picard)
    Replaces the SAMFileHeader in a SAM or BAM file. This tool mak...
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