I have matched tumor-normal samples for targeted sequencing of miRNAs. I wanted to know what are the best filters that I can use to call somatic mutations? What I have planned is, 1. Intersect with germline mutations to retain somatic calls 2. subtract 1000 genomes data 3. Prioritize based on position in miRNA 4. Find out recurrence across samples.
I was wondering, 1. Are their any more filters for biological annotations? 2. What is the best way to get rid of polymorphisms?