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Old 01-31-2012, 01:40 AM   #1
darren.obbard
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Location: Edinburgh, UK

Join Date: Jan 2012
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Default mapping mismatches with Rsamtools, or best approach

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
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