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Old 07-13-2011, 12:54 AM   #1
Zaag
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Location: Amsterdam

Join Date: Nov 2009
Posts: 112
Default Bioscope BAM in BEDtools

I did a whole exome PE run on a SOLiD 4 system. I mapped my reads with both BWA and BioScope to do a comparison.

However, if I run both BAM files in BEDtools coverageBed I get a nice overview for the BWA-BAM. But if I use the same command for the Bioscope-BAM the output says that all coverage is 0

But I know from the IGV that the coverage is the same. Is this known? Is there a solution?
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