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Old 04-08-2012, 07:08 PM   #2
Heisman
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Location: St. Louis

Join Date: Dec 2010
Posts: 535
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I haven't used BWA, but if it is "softclipped" (has an "S" in the CIGAR string) then I'd imagine that guarantees it is mapped (otherwise softclipping doesn't make sense to me). So, it would not be unmapped.

It would be worth checking if the latest version of Pindel will take in softclipped reads. Otherwise, you may want to extract them and feed them into Pindel as unmapped, somehow.
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