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Old 05-05-2014, 06:01 PM   #1
Location: America

Join Date: Jan 2010
Posts: 27
Default How does BWA identify PCR duplicates correctly?

Does it use the usual "same-start-position-for-both-paired-ends" approach? If so, why do many users do this check manually or use picard and the like to do this check instead of just filtering by this flag in the CIGAR string? Am I missing something?
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