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Old 10-11-2011, 12:30 AM   #6
PratikC
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Location: India

Join Date: Sep 2011
Posts: 16
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Quote:
Originally Posted by Heisman View Post
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.
Hi Heisman, I already started mpileup and hopes it will be completed soon. Meanwhile, if possible, can you plz give me some more details of how you set up custom reference sequences and then how you did SNP annotation? You can also mail me if you want to.
Thanks.
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