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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. 4.0.1.0

4.0.1.0

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Tool documentation for GATK release 4.0.1.0

  • BaseQuality
    Median base quality of bases supporting each allele (MBQ) Category ...
  • BaseQualityRankSumTest
    Rank sum test of REF versus ALT base quality scores (BaseQRankSum) ...
  • BaseRecalibrator
    Generates recalibration table for Base Quality Score Recalibration (BQS...
  • BaseRecalibratorSpark (BETA)
    Generate recalibration table for Base Quality Score Recalibration (BQSR...
  • BaseRecalibratorSparkSharded (EXPERIMENTAL)
    BaseRecalibrator on Spark (experimental sharded implementation) Cat...
  • BedToIntervalList (Picard)
    Converts a BED file to a Picard Interval List. This tool provides easy...
  • BQSRPipelineSpark (BETA)
    Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark Catego...
  • BuildBamIndex (Picard)
    Generates a BAM index ".bai" file. This tool creates an index file for...
  • BwaAndMarkDuplicatesPipelineSpark (BETA)
    Takes name-sorted file and runs BWA and MarkDuplicates. Category ...
  • BwaMemIndexImageCreator
    Create a BWA-MEM index image file for use with GATK BWA tools Categ...
  • BwaSpark (BETA)
    BWA on Spark Category Read Data Manipulation Overview...
  • CalcMetadataSpark (BETA)
    (Internal) Collects read metrics relevant to structural variant discove...
  • CalculateContamination
    Calculate the fraction of reads coming from cross-sample contamination ...
  • CalculateFingerprintMetrics (Picard)
    Calculate statistics on fingerprints, checking their viabilityThis tool...
  • CalculateGenotypePosteriors
    Calculate genotype posterior probabilities given family and/or known po...
  • CalculateMixingFractions
    (Internal) Calculate proportions of different samples in a pooled bam ...
  • CalculateReadGroupChecksum (Picard)
    Creates a hash code based on the read groups (RG). This tool creates a...
  • CallCopyRatioSegments (BETA)
    Calls copy-ratio segments as amplified, deleted, or copy-number neutral...
  • CheckFingerprint (Picard)
    Checks the sample identity of the sequence/genotype data in the provide...
  • CheckIlluminaDirectory (Picard)
    Asserts the validity for specified Illumina basecalling data. This too...
  • CheckPileup
    Compare GATK's internal pileup to a reference Samtools mpileup Cate...
  • CheckTerminatorBlock (Picard)
    Asserts the provided gzip file's (e.g., BAM) last block is well-formed;...
  • ChromosomeCounts
    Counts and frequency of alleles in called genotypes (AC, AF, AN) Ca...
  • CigarContainsNoNOperator
    Filter out reads with CIGAR containing N operator Category Rea...
  • CleanSam (Picard)
    Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alig...
  • ClippingRankSumTest
    Rank sum test for hard-clipped bases on REF versus ALT reads (ClippingR...
  • ClipReads
    Clip reads in a SAM/BAM/CRAM file Category Read Data Manipulat...
  • ClusterCrosscheckMetrics (Picard)
    Summary Clusters the results from a {@link CrosscheckFingerprints} run ...
  • CNNScoreVariants (EXPERIMENTAL)
    Apply a Convolutional Neural Net to filter annotated variants Categ...
  • CNNVariantTrain (EXPERIMENTAL)
    Train a CNN model for filtering variants Category Variant Filt...
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