Number of transcript reads with given mutation

Question

[misterie]

Hi,

I have a list with a specific mutations localised on one gene. I have 100 BAM RNA-seq samples, mapped to the reference genome. Let's assume, that I want to calculate number of transcript reads with a specific mutation (SNV), e.g. A/T that is localised at 120 position of gene (e.g. BRCA1). How can I do that? I do not want to do variant calling, just calculate based on mapped BAM file.

Thank you for your tips.

Answer 1

[Pierre Lindenbaum]

convert the cDNA or proteic position to a genomic position: e.g: Getting genomic regions by local coordinates (protein/transcript) How to convert mutation position from gene coordinate to genome coordinate?

and then use something like Coverage In Bam File - Bases And Overall Count ; Finding bases at specific sites using pysam pileup ; ...