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Old 01-24-2012, 09:34 AM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

Starting from pileups? There isn't going to be much software written that's designed to take pileups as input. You have lots more options if you had .bams. SAMtools or BEDTools can both take .bam files and .bed files with your regions, and filter the .bam to only contain reads from those region. BEDTools also has some programs that will calculate coverage for you. So go back to the .bams if you still have them. Otherwise, I think a simple script can do what you want.
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