On Tue, Oct 25, 2022 at 04:25:32PM +0200, Carla Mariner Llicer wrote:
> I'm using Samtools version 1.3.1. I was analysing some illumina paired-end

Please use a modern version.  1.3 is 6 year old, with many bug fixes
and improvements made since then.  This particular issue was fixed in
1.13.

However, also see wish-list item
https://github.com/samtools/samtools/issues/1354 for potential issues
still associated with random selection vs by-quality.

James

-- 
James Bonfield (j...@sanger.ac.uk)
The Sanger Institute, Hinxton, Cambs, CB10 1SA


-- 
 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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