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MuTect unable to detect some germline mutations
Hi, we are testing a custom amplicon kit intended for screening tumor cells, with a Coriell sample. This test was to find out quickly if there are any amplicons that are failed to get coverage. While doing so I also tested if the SNVs overlapping these amplicons from 1KG project are detected using MuTect.
Surprisingly MuTect misses many of the clearly homozygous SNVs, but does detect some others. It is neither called as a KEEP nor REJECT variant. I tried both HC and STD mode to no avail. I am guessing that some filter is completely ignoring this variant, but I am surprised that a clearly homozygous variant would not be called for some extremely low AF background noise. Also, I checked and there are no surrounding variants that MuTect could interpret as a misaligned region. The MQ and base qualities are good.
Please let me know if I am doing something completely wrong here. I am happy to share data snippets if necessary.