I'm wondering how one can extract germline and somatic mutations from the variants calling file.
I have some patients and I have the variants called from both tumor sample and control normal samples for each patient. Basing on these, can I extract somatic mutations and germline mutations for each person?
I thought if I compare the mutation profile within each patient's tumor and normal sample. If mutation A appears in both files then it is a germline mutation, if it appears in tumor sample but not in normal sample, then it is a somatic mutation.
Is this approach correct? Or it is too naive?
Do you have any suggestions/comments for this issue?
Thank you very much!