Hi James, Thank you very much for your explanation.
Best, Li Qian > 在 2017年2月8日，上午12:18，James Bonfield <j...@sanger.ac.uk> 写道： > > Hello, > > On Tue, Feb 07, 2017 at 10:10:55PM +0800, Qian Li wrote: >> I used rmdup within samtools to remove duplicates for paired-end >> reads with default parameters. It turned out that in some cases only >> one mate of a read pair was kept. As I understand, read pairs should >> be kept rather than one mate of pairs is kept. I'll appreciate it very >> much if you could give me some ideas about it. > > I can't help with rmdup, sorry, but will point out that it is not > particularly well supported and has known weaknesses. This is perhaps > a duplicate of this bug: > > https://github.com/samtools/samtools/issues/497 > > For now, I would recommend using either biobambam (C++) or picard > (Java) for this job. > > James > > -- > James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova > | Plurima gyrabant gymbolitare vabo; > A Staden Package developer: | Et Borogovorum mimzebant undique formae, > https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
