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

(MultiSample Mode) Somatic Variants PASSed with zero Normal Coverage

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    David Benjamin

    Zachary Weber this is a good question.  Mutect2 and FilterMutectCalls don't do anything special when there are no normal reads.  It's all the same math, just with any sums over normal reads coming out to zero.  This means that there is less certainty in both directions — we can't rule that that it's germline, but we also can't rule out that it's not germline — and FilterMutectCalls has to try its best under non-ideal circumstances.  In your cases the allele fractions are high enough not to look like artifacts but low enough not to look like germline hets.  This is qualitatively why the variants passed.

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    Zachary Weber

    Thanks for the response, David. This is a peculiar case, and Ideally, we would have good coverage in the normal over all the sites of interest. I think the best course of action would be to annotate, or hard filter these variants in my pipeline.

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