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Old 09-13-2012, 07:12 AM   #6
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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Since a BAM should contain overlapping reads that may or may not agree at any particular base instead of a single sequence then the answer to your question is not straight-forward. First you'll need to generate a consensus sequence via 'samtools', 'bcftools' and 'vcfutils' ... see: http://samtools.sourceforge.net/mpileup.shtml. Having gotten that then you can pull out the bases.

There may be easier ways but that is how I would do it.
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