[BioC] parallel BAM sorting with Rsamtools

Ryan rct at thompsonclan.org
Fri Aug 29 19:36:11 CEST 2014

Hi Jens,

Note that if you have a large number bam files, you can already sort 
them in parallel using BiocParallel or your favorite parallel variant 
of lapply. It's not multi-threaded sorting of single bam files, but it 
will still make use of all your cores.


On Fri Aug 29 10:32:34 2014, Jens Reeder [guest] wrote:
> Hi,
> samtools now allows the sorting of bam files using several threads. This is incredibly useful for large BAM files, e.g. from whole-genome projects.
> Are there any plans of exposing the parallel sorting via Rsamtools' sortBam() and  asBam(..., indexDestination=TRUE)?
> I couldn't find any mention of this in the mailing lists or elsewhere...
> thanks
> Jens
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