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Old 07-08-2010, 02:48 PM   #1
Lee Sam
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Location: Ann Arbor, MI

Join Date: Oct 2008
Posts: 57
Default Supporting Reads in SAMTools SNP Calls

I'm using SAMTools to do some variant calling and I'd like to know how many supporting reads there are for the variant vs the consensus for the SNPs that it calls (like the indel lines). Is there a way to do this that I've missed? I want to use it as a filter on top of the mapping qualities.
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