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Old 10-05-2011, 02:52 PM   #2
aaronh
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Location: California

Join Date: Sep 2008
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First off, you should most likely be mapping to the whole genome. Even if your data is from something like exon capture, you need to know how likely the mapping is to each position in the whole genome. Second, don't use pileup as this is unsupported now. Use mpileup.
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