library mutation profile

[prbndr]

are there any tools that can give me a profile of mutations in my library of mapped sequences reads (using BWA)? i'm specifically interested in obtaining the overall percentage of (A->T, A->G, A->C, T->A, T->C, ...) mutations in my bam/sam file of aligned sequence reads in some sort of matrix/histogram format. any ideas?

i've run across this tool called SAMStat which is somewhat close to what i'm looking for, but not quite.

[swbarnes2]

It's not clear to me how you would distinguish between am A->T mutation and a T->A mutation, or a A->G mutation and a T->C mutation, since you can't tell which strand the mutation happened in.

There's probably a .bam tag that has the variants encoded, but it's probably simpler to make a vcf, then filter that, then count. Samtools or GATK can make vcfs from bams.