Re: [Bio-bwa-help] Illumina quality scores and BWA

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

Samtools has an undocumented option "samtools view -C" that Illumina
quality scores to the standard quality. It assumes Illumina quality is:
log(p/(1-p)). I do not know if this is still true.

Heng

On Tue, Nov 17, 2009 at 01:45:36PM -0800, Benjamin Berman wrote:
> 
> Heng or others,
> 
> Is there an "official" way to convert illumina quality scores into  
> official phred+33 encoding that BWA/SAMTOOLS use?  Of course it's not  
> hard to write a converters oneself, but it would be nice if there were  
> a way to do it within the BWA or SAMTOOLS code base.  I am still using  
> the ill2sanger Maq module contributed by David Cittaro.
> 
> Thanks!
> ben.
> 
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