GATK Team
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Articles
Recent activity by GATK Team Sort by recent activity-
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...
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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 ...
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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...
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CalibrateDragstrModel
estimates the parameters for the DRAGstr model Category Short Variant Discovery Overview Estimates the parameters for the DRAGstr model for an input sample. ...
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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...
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PrintReadsSpark
PrintReads on Spark Category Read Data Manipulation Overview Additional Information Read filters This Read Filter is automatically applied...
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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 ...
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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 ...
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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...
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RenameSampleInVcf (Picard)
This tool enables the user to rename a sample in either a VCF or BCF file. It is intended to change the name of a sample in a VCF prior to merging with VCF files in which one or more...