question about samtools mpileup -6

[bjchen]

Hi,

Can anyone please tell me when to use this option? I am a bit confused about this. I have sequence data with Illumina 1.8 encoding and have aligned them to generate bam files. In the documentation of mpileup, it says

-6 Assume the quality is in the Illumina 1.3+ encoding.

But I don't know if bam files have such encoding issues..

Thanks!!!

[Kennels]

I think it means if you have the qscores in the former illumina format then use this option. Since your data is based on Illumina 1.8+ which i believe is in the Sanger qscore format already, then you don't need to use it.
Here is a reference explaining qscore differences:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/

[bjchen]

That's what I guessed, although still got confused by the "+" in the "1.3+"...
Thanks!