Need Clarification On The Formula For Base Alignment Quality (Baq) When Computed Via Mpileup

Question

[tomislav.ilicic]

Dear all,

I am trying to compute the offset to base alignment quality (BAQ) myself from mpileup files (using this parameters -l $bed_file -BQ 0 -A -d10000000).

After some bit of research I have found this formula:

At the i-th read base, BAQi = Qi - (BQi - 64) where Qi is the i-th base quality.

I have following questions:

• Is Qi the Phred Score P = 10^( -Q/10) of the base? Q being ascii_val(char) - 33 (if Sanger format).
• Is BQi the same as Qi?
• And do you always have to subtract with 64 BQi -64 or is it depended on the sequencer used?

I would really appreciate some help.

Thanks.

Answer 1

[Istvan Albert]

The computation of BAQ is described in Improving SNP discovery by base alignment quality (Bioinformatics, 2010).

To be honest I don't understand it beyond noting that it does not quite look like your formula.

[tomislav.ilicic]

Thanks, actually that is useful. But I agree, if they use a HMM to calculate BAQ than this is not at all what the formula says - looks much easier. The formula is described on page 6 in here http://samtools.sourceforge.net/SAMv1.pdf