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Old 04-22-2010, 03:21 PM   #1
bbimber
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Location: wisconsin

Join Date: Jan 2010
Posts: 12
Default bwasw: get SAM output containing all hits per query?

when running bwasw (not bwa aln) is it possible to produce a SAM output containing all matches per read, not just one hit? i've seen a number of posts asking this question about bwa aln, but have not seen it about bwasw. these two seem to produce distinct outputs, with bwasw producing a SAM file directly.

thanks for any help.
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