GATK Team
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Articles
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How to setup and use temporary folder for GATK local execution
GATK tools like many other bioinformatics software rely on temporary files created during execution. However unlike other tools that may use the immediate output folder for temporary files such as ...
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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...