Germline and somatic SNPs in same or different allele

Question

[Nacho del Valle]

Dear community,

I have access to germline and somatic vcf files for a cohort of patients (each patient has a vcf file with germline snps and a somatic vcf file with somatic snps).

I need to know if certain germline snps are in the same allele as certain somatic snps (i.e is germline snp A in the same allele as somatic snp B for patient 1?).

I am aware of phasing tools such as shapeit, but I am not sure if that is the right approach (do I need to phase germline and somatic vcf files independently or do I need to merge them and phase them?).

I'm sorry if this is very basic, but I have no idea if this would be the right approach to my question. Do you have any suggestions about the best tool to use?.

Thanks in advance for the help!

Answer 1

[iraun]

Hi!

Concatenate each patient's germline and somatic VCF files, and then run a phasing tool. You mentioned shapeit, I have used whatshap for this very same purpose, but maybe shapeit could work too :)

[Nacho del Valle]

Hi,

Thanks a lot for the answer- that is the approach I will try!