I have identified somatic mutations with MuTect from WES data from paired normal and tumor samples, and am trying to view with IGV the sequences around the genomic location where somatic mutations are identified. I got 2 questions:
(1) Is it absolutely not tolerable if there is even one sequence from normal sample that shows mutation at the genomic location where somatic mutation is identified by MuTect software?
(2) There are noise like mutations at the genomic locations that are not identified as somatic mutation by MuTect. Does this indicate any thing about data quality, or any thing?