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GATK4 MuTect2 passing germline events?
Dear GATK team,
I have been experimenting with calling somatic variants in my tumor/normal WES data using GATK4 MuTect2. After calling and filtering, I found many sites (mostly indels and MNP indels) passing filters that were also clearly present in the normal, and even were listed as having a high AF in the normal. This really surprised me, because I thought that by default, MuTect2 applied:
--max_alt_allele_in_normal_fraction 0.03 --max_alt_alleles_in_normal_count 1
I went back and investigated the header of my VCF files, and I don't see those options anywhere. Should these be being applied by default, or do I need to pass them in by hand in the new version? I also looked at FilterMutectCalls, but didn't see anything for filtering sites present in the normal.
Thanks for your help!