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Old 09-12-2011, 12:36 PM   #1
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Default library mutation profile

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.
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Old 09-12-2011, 02:15 PM   #2
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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.
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