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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?