I need to verify that BWA takes into account mate pair data, and the BWA paper that I found seems to be somewhat ambiguous in how it derives mapping quality for these paired reads. If someone could point me at some source code or describe how BWA deals with paired data that would be extremely helpful.
Also, I would feel much happier if I knew how the actual implementation of this statement from the paper worked:
Again if someone could give a little bit of a more detailed explanation or point me at the source code file (or both) I would be very happy.
Also, I would feel much happier if I knew how the actual implementation of this statement from the paper worked:
BWA assigns a Phred-like quality score to each read (MapQ) based on match uniqueness, sequence identity, end-pairing, and insert size that is intended to indicate confidence of read placement accuracy in the genome
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