Re: [Samtools-help] sort sam file using samtools sort

[Robert D. <rm...@sa...>]

On Wed, 31 Jan 2018, Yogesh Gupta wrote:

> Can I use samtools sort to sort sam file by read name directly?
>
> samtools sort -O sam -n -o sample.sort.sam sample.sam

Yes, that should work.

>
> I am using samtools version 1.4

I'd recommend upgrading to the most recent version (1.7).  Sort has had a 
few improvements.  Among other things, it's much better at using the 
amount of memory it's supposed to than it used to be.

Rob Davies              rm...@sa...
The Sanger Institute    http://www.sanger.ac.uk/
Hinxton, Cambs.,        Tel. +44 (1223) 834244
CB10 1SA, U.K.          Fax. +44 (1223) 494919


-- 
 The Wellcome 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.