I have tumor and normal samples. When running a somatic caller, the output vcf file contains a column named 'Filter' which has two values:
- Pass: which means that this variant is Somatic
When the Filter is 'Rejected', does this mean that the variant is Germline ? or we cannot really distinguish this?
What I need to do is, I have tumor and normal samples, and I need to check which germline TP53 variants in the normal sample are also present in the tumor cell. Is my above approach valid? i.e.
first identify all the germline TP53 variants in the normal sample
run the somatic caller on the tumor vs normal samples
check the output vcf of the somatic caller, and scan my germline TP53 set of variants against it, if a variant in the latter set is found in the vcf and annotated as rejected, this means that this germline mutation exists in the tumor cell
What do you think about this?