Also trying to sort through what looks to be an issue with using pileup for SNP calling in the 10 column format. Column 3 is the reference base and column 4 is the consensus base. I have numerous examples where reference base = consensus base with a breakout of the number of A T C G represented as a count. For aaChanges I need an input line for each non-zero count of A T C G from the pileup report to test which of those SNPs would actually result in an amino acid change. Doesn't seem to be an easy thing to do in Galaxy.
Any recommendations on how others are doing SNP calling from exome data and detecting amino acid changes? Does anyone have a published workflow they would recommend or could share?
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