I had previously performed Mutect2 to detect variants (normal-tumor comparison). However, if I load the BAM files to view the variants, most of the variants display the same mutation in both tumor and normal sample. Probably in a slightly higher frequency in the tumor sample (by visual gauging).
I am trying to identify variants that are not present in the normal (<2%) but only in the tumor samples (>20%). How do I do this analysis? I have looked through the VCF files for this information but could not find any direct correlates. Is there something that I am missing or will I have to rerun the analysis using different parameters? Such as altering --normal-lod or --minimum-allele-fraction. If so what would be the value that you would suggest to set for these parameters? Thank you very much.
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