Removing of dupliications of mate pair reads after mapping

Krosh · 05-13-2014, 08:12 AM

Could anybody say what tool I should use for removing of duplications of mate pair reads after mapping?

Thank you.

blancha · 05-13-2014, 08:30 AM

gt1 · 05-14-2014, 01:43 AM

In my experience the following do the same thing as the Picard duplicate marking/removal and are somewhat faster:

biobambam bammarkduplicates2 (see https://github.com/gt1/biobambam)
bamUtil dedup (see http://genome.sph.umich.edu/wiki/BamUtil). May be slightly faster than biobambam at duplicate marking/removal, but has problems with very high depth files.

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05-13-2014, 08:12 AM	#1
Krosh Junior Member Location: Russia Join Date: Feb 2011 Posts: 8	Removing of dupliications of mate pair reads after mapping Could anybody say what tool I should use for removing of duplications of mate pair reads after mapping? Thank you.

05-14-2014, 01:43 AM	#3
gt1 Junior Member Location: Cambridge, UK Join Date: Jul 2013 Posts: 9	In my experience the following do the same thing as the Picard duplicate marking/removal and are somewhat faster: biobambam bammarkduplicates2 (see https://github.com/gt1/biobambam) bamUtil dedup (see http://genome.sph.umich.edu/wiki/BamUtil). May be slightly faster than biobambam at duplicate marking/removal, but has problems with very high depth files.

05-13-2014, 08:30 AM	#2
blancha Senior Member Location: Montreal Join Date: May 2013 Posts: 367	http://picard.sourceforge.net/comman...MarkDuplicates