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-   -   bwasw: get SAM output containing all hits per query? (http://seqanswers.com/forums/showthread.php?t=4816)

bbimber 04-22-2010 04:21 PM

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.

lh3 04-22-2010 06:10 PM

Sorry, this is not possible by design.


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