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CalculateGenotypePosteriors shouldn't modify GTs with no data #5666

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ldgauthier opened this issue Feb 12, 2019 · 0 comments
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CalculateGenotypePosteriors shouldn't modify GTs with no data #5666

ldgauthier opened this issue Feb 12, 2019 · 0 comments
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@ldgauthier
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A user reported that CalculateGenotypePosteriors generated a bunch of "new" variants (https://gatkforums.broadinstitute.org/gatk/discussion/comment/56226). What happened was that no-calls that look like GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 became GT:AD:DP:GQ:PL:PP 0/1:0,0:0:,:30,0,30 or similar when a high AF prior was applied. The expected behavior is for PPs to not be applied and the GT to remain no-call.

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