Read counts at specific locations in SAM files

Question

[fogarty.mc]

I have sam files created using hisat2 of RNAseq reads assembled to a reference of 7 genes (not whole genome). What I need to be able to do is for a given position in the assembly I need too: 1. Count the total # of reads at that position 2. Count of reads of each nucleotide at that position

I have ~30 Rnaseq libraries and ~70 positions I need to assay. This was done in a allohexaploid species so I am looking at positions know to be polymorphic between genomes.

Any ideas of how best to do this?

[GenoMax]

bam-readcount will do this for you. Samtools depth/mpileup would be other options.