Re: [Samtools-help] samtools and picard - removing duplicates

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

Hi John,

Samtools and picard use very similar algorithms.  The major difference IIRC is that picard’s MarkDuplicates works for inter-chromosomal pairs whereas samtools restricts itself to pairs where both ends map to the same chromosome for performance reasons.

-t

On Sep 22, 2014, at 5:07 PM, John Duce <joh...@gm...> wrote:

> Dear Samtools Gurus,
> 
> I did a lot of googling and looking through the code but I couldn't find anything definitive about my question. It is my understanding that samtools rmdup removes duplicates based on position only, whereas picard MarkDuplicates marks duplicates based on position and sequence. Is this correct? 
> 
> John Duce
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