samtools Mpileup quality scores?

Question

[AW]

Dear all,

What is the default quality scores expected by samtools mpileup?

I see you can specify the option

-6, --illumina1.3+ Assume the quality is in the Illumina 1.3+ encoding.

Is the default therefore Sanger?

And what do you specify if you have Illumina 1.9 where the quality scores are different to Illumina 1.3??

Thanks!

[AW]

Sorry I should have been clearer.

Does it expect phred33 or phred64?

Answer 1

[Istvan Albert]

All modern tools will expect Sanger encoding. It is best to convert all data to that.

See also:

Convert Illumina Reads To Sanger Score

[AW]

Thanks I meant does it expect Sanger phred33, illumina 1.3 phred 64 or illumina 1.8 phred 33?

[Istvan Albert]

sanger = sanger phred33 encoding

https://en.wikipedia.org/wiki/FASTQ_format

[AW]

Thanks!

So how do I specify illumina phred33?

[Istvan Albert]

actually most of the time you may not even need to do anything for illumina phred 33 data

the offset is the same, 33, that is what throws tools off,

the encoding differs only in the largest value 40 vs 41 that on its own matters only if someone wrote a very sloppy tool that can't think outside of 40