Re: [Samtools-help] Question about samtools mpileup and overlapping reads [EXT]

[James B. <jk...@sa...>]

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

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James Bonfield (jk...@sa...)
The Sanger Institute, Hinxton, Cambs, CB10 1SA


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