MuTect2 AD does not match AF

I am seeing issues with the allelic depths and allelic frequencies/fraction reported in some of our variants. For example:

Chr Start End Ref Alt POS REF ALT QUAL NORMAL.AD NORMAL.AF TUMOR.AD FREQ TUMOR.AD.TOTAL NORMAL.AD.TOTAL chrX 152482917 152482917 T C 152482917 T C 986.47 79,0 0.02 436,443 0.503 879 79

Any idea what is going on? In this case, the Normal sample AF is reported as "0.02", or 2%, but it also reports that the Normal sample has 0 alt reads. How can you have a variant frequency when there are no reads? I have seen this occurring as well for the tumor samples; how could you have a variant at all when there are no reported alternate reads for the variant?

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  • steve1steve1 Member

    Thanks David. We do not use recent releases. We are locked into GATK 3.8. Are there any guidelines on how we can deal with this?

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    Oh boy, 3.8. None of us were on the M2 team then, and M2 back then wasn't even beta yet. I would use a more recent release if at all possible. GATK 3.8 will probably cost you about three times as many false positives with worse sensitivity, too. The need for reproducibility may override that, of course, but it's worth knowing how big the difference is.

    Also, it may be more feasible than you would think to re-run all of your samples through GATK 4.1. M2 is about ten times as fast as in GATK 3 and the cost for the whole pipeline of a typical WGS pair is a dollar or two (in Google cloud fees) on Firecloud.

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