Extract somatic mutations and germline mutations from variant calling files?

Question

[ginnyli056]

Hi all,

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!

Answer 1

[Emily]

Germline: compare the normal cells to the reference genome.

Somatic: compare the tumour sample to the normal sample from the same person.