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Old 05-06-2014, 12:13 PM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

The flag in the cigar string is left 0 by default, and is only changed if a piece of software changes it. I'm pretty sure bwa does not check for this, so the fact that the flag is unset by bwa doesn't means that bwa actually determined that the read is not a PCR duplicate.
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