Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Ion torrent PCR duplicates DavyK Bioinformatics 0 08-29-2013 03:14 AM
Ignore PCR Duplicates in CollectTargetedPcrMetrics fongchun Bioinformatics 5 02-16-2013 03:51 PM
PCR duplicates aquleaf RNA Sequencing 5 10-30-2012 11:40 AM
PCR duplicates questions slny Bioinformatics 8 06-07-2011 04:06 AM
Picard MarkDuplicates - How to identify duplicates in generated BAM file makarovv Bioinformatics 6 11-10-2010 09:02 AM

Thread Tools
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?
sowmyai is offline   Reply With Quote
Old 05-06-2014, 12:13 PM   #2
Senior Member
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.
swbarnes2 is offline   Reply With Quote

bwa, cigar, pcr duplicates, sam flag

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:22 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO