I used a VCF file to filter somatic mutations based on various various filters as suggested by vendor such as Pass/ Fail based on somatic score, quality score, read depth etc. I ma down to around 50 variants which has various different functions and are map to different genomic locations - introns, exons, promoter etc. some of them are predicted to be associated with loss of function while other will not affect any such change. The question, I am struggling with is which variants may be important to report or validate. Are only exonic variants important or I should report the once which are associated with loss of function. The data is comparing matched normal vs tumor samples with underlying aim to identify the disease associated genes. Any suggestion or pointers, links to study further will be helpful.