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Old 04-18-2011, 07:56 PM   #2
jstjohn
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Location: San Francisco, CA

Join Date: Jun 2010
Posts: 35
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1. I think GATK uses the Read Group tag to partition the data into separate organisms for variant calling. If you want them treated as the same sample then you give them all the same read group tag, while if you want them treated differently then give them different read group tags. I am actually not 100% sure that "read group" is the right tag for this, so someone please correct me if thats not the case.

There is a program in the Picard package to manipulate the read group along with other tags in bam files.

2. Read through this page which describes the different suggested protocals in order of how good they are thought to perform vs computational time involved. I think the best (and slowest) option is to pool everything. The page gives a good overview of the suggested set of steps to follow to call variants given different computational commitments:
http://www.broadinstitute.org/gsa/wi...th_the_GATK_v2
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