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Old 09-24-2012, 08:38 AM   #2
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Location: Seattle

Join Date: Jun 2011
Posts: 1
Default Try pysam

I dealt with a similar issue, and the solution I came to was to use pysam (python module) to parse SAM/BAM files directly, rather than trying to make sense of mpileup files after the fact. Pysam will allow you to call samtools pileup and return the results in small chunks that you can do what you want with.

Take a look at this topic, and perhaps pysam in general. If python isn't your cup of tea, this is a general approach that other languages have implemented.

good luck.
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