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Old 04-19-2011, 12:29 PM   #4
Location: United States

Join Date: Sep 2008
Posts: 27

Originally Posted by newbietonextgen View Post
can you actually distinguish which BAM file gave rise to particular SNPs?
If you are doing multi-sample calling with each sample in a separate BAM, it doesn't always make sense to say that one BAM file gave rise to a particular SNP. For example you could have three samples each of which has weak evidence for a particular SNP: not enough to call the SNP if you are analyzing the samples separately but when you pool them together the combined evidence is sufficient to call a SNP.
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