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Somatic Mutations In Microrna Genes

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

mirna somatic
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updated by Chris Miller Chris Miller • written by nro • nro

1 answer

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.

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written by Chris Miller Chris Miller

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