Re: [Samtools-devel] @RG header tag (relevant to 1.3 Draft)

[Heng Li <lh...@sa...>]

On Aug 25, 2010, at 9:39 AM, Keiran Raine wrote:

> Hi all,
> 
> I've just come to write some code and thought to myself, wouldn't it  
> be useful if 'read length' was a tag in the @RG header lines.
> 
> I expect there are a few things to check
> 
> 1. Is it likely that a RG would not have fixed read length?

454/Sanger/Helicos/PacBio reads are variable in length.

> 2. Should it be enforced and validated if defined?

So this cannot be a mandatory tag.

> 3. RL seems a sensible tag, any objections?

But it is a sensible tag for Illumina/SOLiD. We may redefine it as "average read length" which is useful information without going through the alignments.

Heng

> 
> Has this been previously shot down in flames?  I did check though past  
> emails (but I could have missed it).
> 
> Regards,
> 
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> kr...@sa...
> 
> 
> 
> 
> 
> 
> 
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-- 
 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.