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Mutect2 genotype-germline-sites filtering discrepancy

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    Genevieve Brandt (she/her)

    Hi TA,

    What version of GATK did you run with this comparison?

    Thank you,

    Genevieve

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    TA

    Hi,

    I used gatk 4.2.0.0

    We ran on terra referencing broad gatk docker us.gcr.io/broad-gatk/gatk@sha256:f2602e0bbc0117c30d23d8d626eb8d0a21ca672bb71180b5cf25425603a0ae09 

     

     

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    David Benjamin

    TA The issue with the clustered events and haplotype filters when running in -genotype-germline-sites is a real problem.  These filters should only be triggered by a cluster of technical artifacts or somatic variants, not by germline variants.  However, since the default mode of Mutect2 ignores most germline sites, we overlooked this possibility.  We need to fix those filters so that they work as intended.

    I can't think of a reason for the strand bias filter.  For the calls that have the strand bias filter with default settings and then pass when genotyping germline sites, are there any other filters applied in default mode?

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    Genevieve Brandt (she/her)

    Hi TA, I have created a github issue ticket so that our developer team can continue to look into this filtering discrepancy that you brought up. Here is the link where you can follow along with the progress: https://github.com/broadinstitute/gatk/issues/7391.

    Could you submit example data demonstrating these discrepancies to our ftp site following these instructions: https://gatk.broadinstitute.org/hc/en-us/articles/360035889671? 

    Thank you,

    Genevieve

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