SEQanswers - View Single Post - How does BWA identify PCR duplicates correctly?

sowmyai · 05-05-2014, 06:01 PM

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?

05-05-2014, 06:01 PM	#1
sowmyai Member Location: America Join Date: Jan 2010 Posts: 27	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?