I am now trying to identify germline mutations from tumor and matched normal samples in TCGA and also I need to know this germline mutation occur in exactly which samples. I know some software like VarScan can do this, but they are all working on .bam file, I only have some .vcf files, any software or protocol can do the following? 1. Identify germline mutation in a group of tumor and matched normal. 2. For each of germline mutations identified, tell which sample they call.
Thanks in advance!