Re: [Samtools-help] Parallelization of samtools

Yes, sorting takes too long and it would be good if it can be multi-threaded. I would love this feature as well. Colin from novocraft has recently implemented a multithreaded BAM sorting, but I do not know if the binary is free.

Heng

On Feb 6, 2012, at 10:44 AM, Lorenzo Pesce wrote:

> Hi -
> 
> I am trying to structure a pipeline to be run on a parallel supercomputer. My issue is that I haven't found an effective way to run the sorting in parallel (except rewriting the sorting part of the code).
> 
> I was trying to find whether i can first split a sam file and then sort it, but it does not seem to be possible. I was trying an approach like 
> 
> samtools view <aligned file from paired reads>.sam -S -b -o <output>ch1.bam chr1
> 
> Are there approaches that allow one to do such a calculation or at least use parallelization in some other way for this step?
> 
> Thanks a lot in advance,
> 
> Lorenzo
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