Re: [Samtools-help] remove duplicates belonging to different RG

[Tim F. <tfe...@br...>]

The way Picard handles this is actually by looking at the LB (library) tag on the read groups.  It will treat reads from the same library as one group for duplication detection, but will not call things duplicates when the reads originate from different libraries.  So if the LB tag on your read groups is the same they'll be merged for duplicate detection, and if it's different they won't be.

-t

On Feb 28, 2011, at 8:32 AM, Davide Cittaro wrote:

> Hi all, how does samtools (and picard) deal with possible duplicates that belong to different RG within the same BAM file? Are they kept (because they come from different groups) or deleted (because they are likely to be duplicates)? I'm asking this because I have a sample that has been run on two lanes on the same flowcell, therefore I can have duplicates but I want to keep lane information in RG field.
> 
> Thanks
> 
> d
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