mapping mismatches with Rsamtools, or best approach

[darren.obbard]

Hi,

Given a bam file, I wish to identify the mismatches (state and position, ie. A->T at 21) between my mapped reads and my reference. Note that I want the differences on a per read basis, not on a per reference basis (e.g. SNPs)

I had hoped to use R to do this, using Rsamtools. However, as far as I can see Rsamtools does not parse the mismatch information (state,location) only the 'cigar'. Indeed, its not clear to me how one would get this information from the bam file.

Am I misunderstanding?

Given a bam file, what is the best R approach to use?

Thanks,

Darren