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04-22-2010, 04:21 PM
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#1 |
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Member
Location: wisconsin Join Date: Jan 2010
Posts: 12
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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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04-22-2010, 06:10 PM
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#2 |
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Senior Member
Location: Boston Join Date: Feb 2008
Posts: 693
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Sorry, this is not possible by design.
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