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!