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
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