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GATK Team

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Recent activity by GATK Team Sort by recent activity Recent activity Votes
  • QualityYieldMetrics

    Back to Tool Docs Index Metrics Category Metrics Overview A set of metrics used to describe the general quality of a BAM file This table summar...

  • CheckPileup

    Compare GATK's internal pileup to a reference Samtools mpileup Category Diagnostics and Quality Control Overview Compare GATK's internal pileup to a reference Samt...

  • CreateSomaticPanelOfNormals (BETA)

    Make a panel of normals for use with Mutect2 Category Variant Filtering Overview Create a panel of normals (PoN) containing germline and artifactual sites for use ...

  • FilterVariantTranches

    Apply tranche filtering Category Variant Filtering Overview Apply tranche filtering to VCF based on scores from an annotation in the INFO field. The annotation ca...

  • CalibrateDragstrModel

    estimates the parameters for the DRAGstr model Category Short Variant Discovery Overview Estimates the parameters for the DRAGstr model for an input sample. ...

  • PrintReadsSpark

    PrintReads on Spark Category Read Data Manipulation Overview Additional Information Read filters This Read Filter is automatically applied...

  • ASEReadCounter

    Generates table of filtered base counts at het sites for allele specific expression Category Coverage Analysis Overview Calculate read counts per allele for allele...

  • CountBasesSpark

    Counts bases in the input SAM/BAM Category Coverage Analysis Overview Calculate the overall number of bases SAM/BAM/CRAM file Input A single BAM file ...

  • CountReadsSpark

    Counts reads in the input SAM/BAM Category Coverage Analysis Overview Calculate the overall number of reads in a SAM/BAM file Input A single BAM file ...

  • ReadAnonymizer (EXPERIMENTAL)

    Replace bases in reads with reference bases. Category Other Overview Replace bases in reads with reference bases. Used to anonymize reads with information from t...