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Old 12-07-2011, 07:33 AM   #1
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Location: New York

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Default BWA and mate pair

Do newer version of bwa support mate pair library

We aligned mate pair libraries with novo align and bwa and got quite different results.
Novo align results seem to make sense we get large insert pairs oriented reverse/forward and small insert pairs (contamination) oriented forward/reverse.

In the case of bwa we get large insert size oriented forward/reverse which suggest that bwa is able to align mate pair, but we get a complex distribution of insert size for reverse/forward pairs.
Is there any documentation on how bwa deals with mate pair?
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