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Old 07-20-2011, 04:45 AM   #1
Graham Etherington
Location: Norwich, England.

Join Date: Apr 2010
Posts: 22
Default Extract perfectly mapped reads from SAM/BAM file

Given a SAM or BAM file, does anyone know how to identify which paired-sequences map perfectly to the reference? By perfectly mapped, I mean that the query is identical to the the reference (or its reverse complement).
I'm fine using either command-line tools or programming.
Many thanks,
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