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Old 10-09-2011, 07:42 PM   #5
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
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Pileup should not take that much time. Since you are going to try mpileup, as it is running you can check to see how far it has progressed. Assuming you sort your bam file prior to running it you'll be able to guess how long it will take.

If it's still acting weirdly, write back. I've set up custom reference sequences for this purpose (although I use Novoalign, not BWA, to align) and made it work fine.
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