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Old 07-07-2010, 05:18 AM   #4
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Location: Boston

Join Date: Feb 2008
Posts: 693

It cannot be 45 mismatches. It must be soft clipping.

For PE reads, bwa runs SW alignment for unpaired mate. SW is much more permissive. This procedure is rewritten in the paper, not phantom. You may filter the alignment if you do not like them.
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