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Old 09-26-2013, 12:41 PM   #1
Location: Birmingham, Al

Join Date: Feb 2010
Posts: 39
Default BWA & multiple alignments per read

Bowtie clearly indicates in its manual that it will randomly assign any read for which there are multiple equally valid alignments. I can not see any such discussion regarding the "mem" aligner for BWA. Can anyone tell me how BWA handles multiple alignments per read, and what the default settings are?
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