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

Join Date: Jun 2008
Posts: 1,104

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: Having gotten that then you can pull out the bases.

There may be easier ways but that is how I would do it.
westerman is offline   Reply With Quote