Tweet
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?
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?