Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!
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!