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

Using uninformative reads (DP) in Mutect2


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    David Benjamin

    This is not the output of Mutect2 / FilterMutectCalls.  If you give us an example as it appears in the VCF output of FilterMutectCalls we might be able to diagnose the issue.  Also, gt_AD is not a GATK annotation so we can't offer an opinion on it.  If there is a discrepancy between DP and AD we can try to explain it.

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