I am working on somatic mutation identification in mouse. The mouse strain I am working on is different than mm10 so it has a lot of germline SNPs. I am trying to call somatic mutation in tumor vs matched normal control. However, I found that all "PASS" mutations have 0/0 genotype in normal sample (which means they all have the same alleles as the reference genome). And after reading mutect2 document and paper, I find mutect2 is calling samples against reference genome first and consider (and remove) sites with alleles in normal samples different than genome as germline mutation. So they will not go to somatic mutation calling.
The question is: is there a way to identify somatic mutation at the site with non reference allele in normal samples? For example, The site in reference genome is C. Normal sample genotype is "G/G"(which is because of strain difference than mm10 mouse strain), and somatic mutation in Tumor sample is T.
Please sign in to leave a comment.