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 r...@sanger.ac.uk
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.
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