On 5 Sep 2014, at 06:52, Adam Skarshewski <[email protected]> wrote:
> Running into a problem with samtools 1.0 sort, specifically the merging
> phase. It's very slow compared to the previous version. I have a 965MB bam
> file (which is already sorted)
Does your BAM file have rather a lot of reference sequences? There is a known
problem in the new header merging [1] that we are working on fixing, that
happens when sorting/merging files mapped to thousands of contigs.
John
[1] https://github.com/samtools/samtools/issues/260
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
------------------------------------------------------------------------------
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
