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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. 4.0.2.0

4.0.2.0

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Tool documentation for GATK release 4.0.2.0

  • CNNVariantWriteTensors (EXPERIMENTAL)
    Write variant tensors for training a CNN to filter variants Categor...
  • CollectAlignmentSummaryMetrics (Picard)
    Produces a summary of alignment metrics from a SAM or BAM file. This t...
  • CollectAllelicCounts (BETA)
    Collects reference and alternate allele counts at specified sites C...
  • CollectBaseDistributionByCycle (Picard)
    Chart the nucleotide distribution per cycle in a SAM or BAM fileThis to...
  • CollectBaseDistributionByCycleSpark (BETA)
    Collects base distribution per cycle in SAM/BAM/CRAM file(s). Categ...
  • CollectFragmentCounts (BETA)
    Collects fragment counts at specified intervals Category Cover...
  • CollectGcBiasMetrics (Picard)
    Collect metrics regarding GC bias. This tool collects information about...
  • CollectHiSeqXPfFailMetrics (Picard)
    Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory in...
  • CollectHsMetrics (Picard)
    Collects hybrid-selection (HS) metrics for a SAM or BAM file. This too...
  • CollectIlluminaBasecallingMetrics (Picard)
    Collects Illumina Basecalling metrics for a sequencing run. This tool ...
  • CollectIlluminaLaneMetrics (Picard)
    Collects Illumina lane metrics for the given BaseCalling analysis direc...
  • CollectIndependentReplicateMetrics (Picard) (BETA)
    Estimates the rate of independent replication rate of reads within a ba...
  • CollectInsertSizeMetrics (Picard)
    This tool provides useful metrics for validating library construction i...
  • CollectInsertSizeMetricsSpark (BETA)
    Collects insert size distribution information on alignment data Cat...
  • CollectJumpingLibraryMetrics (Picard)
    Collect jumping library metrics. This tool collects high-level metrics ...
  • CollectMultipleMetrics (Picard)
    Collect multiple classes of metrics. This 'meta-metrics' tool runs one...
  • CollectMultipleMetricsSpark (BETA)
    Runs multiple metrics collection modules for a given alignment file ...
  • CollectOxoGMetrics (Picard)
    Collect metrics to assess oxidative artifacts.This tool collects metric...
  • CollectQualityYieldMetrics (Picard)
    Collect metrics about reads that pass quality thresholds and Illumina-s...
  • CollectQualityYieldMetricsSpark (BETA)
    Collects quality yield metrics from SAM/BAM/CRAM file(s). Category ...
  • CollectRawWgsMetrics (Picard)
    Collect whole genome sequencing-related metrics. This tool computes me...
  • CollectReadCounts (BETA)
    Collects read counts at specified intervals Category Coverage ...
  • CollectRnaSeqMetrics (Picard)
    Produces RNA alignment metrics for a SAM or BAM file. This tool takes ...
  • CollectRrbsMetrics (Picard)
    Collects metrics from reduced representation bisulfite sequencing (Rrbs...
  • CollectSamErrorMetrics (Picard)
    Program to collect error metrics on bases stratified in various ways. S...
  • CollectSequencingArtifactMetrics (Picard)
    Collect metrics to quantify single-base sequencing artifacts. This too...
  • CollectTargetedPcrMetrics (Picard)
    Calculate PCR-related metrics from targeted sequencing data. This tool ...
  • CollectVariantCallingMetrics (Picard)
    Collects per-sample and aggregate (spanning all samples) metrics from t...
  • CollectWgsMetrics (Picard)
    Collect metrics about coverage and performance of whole genome sequenci...
  • CollectWgsMetricsWithNonZeroCoverage (Picard) (BETA)
    (Experimental) Collect metrics about coverage and performance of whole ...
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