Does someone has experience in filtering somatic variants from SVtyper-genotyped VCF files produced with lumpy (WGS, 30-50x)? Lumpyexpress was run as instructed in the manual, and the VCF was genotyped with SVtyper, everything on default settings. There are some issues on Git on how to discriminate somatic from germline variants, but still I did not really make progress in how to filter out the somatics. Anyone experienced in this?
EDIT: Ryan Layer was so kind to give this response on Github:
Select the variants that are non reference in your tumor and have no evidence in the normal. You can use SnpSift to do this with something like: GEN.GT != 0/0 && GEN.AO == 0 The syntax is not exactly right. Check here for the exact details.