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Old 01-09-2012, 11:39 AM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

You could make a pileup, which would have the depth at every point. Then some kind of script to make a .bed file of all those windows you wanted, and you can apply the .bed file to the .bam with samtools view to get a .bam just at those coordinates.

You could probably use BEDTools to do much of that. I'm not sure there's an easier way.
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