Somatic Mutations In Microrna Genes

Question

[nro]

HI,

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?

Thanks

Answer 1

[Chris Miller]

You should probably use a somatic mutation caller, rather than calling tumor and normal separately, then trying to filter out germline events. Varscan, Somatic Sniper, GATK, Strelka, and many other tools will do this.