frequency of each nucleotide at each position in sequence

Question

[Sara]

I have aligned RNAseq data and now I have bam files for control and treated conditions. I am trying to get the frequency of each nucleotide at each position in a sequence of 95 nt. to get the mutation rate at each position. except for the igv, is there any way to do that?

[Medhat]

I think you are referring to calling variant ?!
something like:

https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq

Answer 1

[george.ry]

If you're not looking to call the variants as Medhat says, then bam-readcount will do this.