Identify reads aligned to mutant and wild type sequences

[rpauly]

Hi, Is there a way to identify the number of reads that aligned to the mutant and wild type sequences using bam-readcounts? Thanks!

[chrisamiller]

Yes, assuming that you know the location of informative sites in the genome, querying that position with bam-readcount will return the counts of each base at that location and allow you to count wild type or mutant reads.