I found some single point mutation (or RNA editing, I don't know) in my RNAseq. I want to classify those alterations... I mean, I want to know every position where they happen and teh type of alteration.
What is the best way to do that? Is it possible to use GATK (Broad Institute) to analyse this kind of data (even though it was not properly created for RNAseq analysis)?
Thank very much for any help