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

Mutect2 -- How is the --max-population-af filter used in tumor-only mode?


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    David Benjamin

    This parameter is a performance optimization in the active region code.  It is not an argument of FilterMutectCalls.  It is possible that a different site near this one will be considered active and trigger assembly and genotyping of the surrounding area, including the site in question.  Then FilterMutectCalls uses the full germline probability model to decide whether to keep a variant.  In this case, perhaps despite the large population AF the allele fraction in the sample was low enough that it did not appear to be germline.

    Regardless, one should never take tumor-only calls too seriously.  Even if one aggressively filtered out everything in gnomAD tumor-only calls are inevitably full of rare germline variants.

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