I don't know how to make MAF file for Genome MuSiC. My protocol is below.
Normal Samples Exome Analysis
(BWA->GATK->Normal Samples' Group Annotation info.)
Tumor Samples Exome Analysis
(BWA->GATK->Tumor Samples' Group Annotation info.)
Make MAF file
(Tumor Annotation info.) \ (Normal Annotation info.)
in other words, the relative complement of Normal Annotation set in Tumor Annotation set
Is this correct? or simply, use only Tumor Annotation info.?
if you know best practice, could you tell me that?