Question: Need Clarification On The Formula For Base Alignment Quality (Baq) When Computed Via Mpileup
gravatar for tomislav.ilicic
6.7 years ago by
United Kingdom
tomislav.ilicic120 wrote:

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.


samtools sam • 2.2k views
ADD COMMENTlink modified 6.7 years ago by Istvan Albert ♦♦ 84k • written 6.7 years ago by tomislav.ilicic120
gravatar for Istvan Albert
6.7 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Istvan Albert ♦♦ 84k

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

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by tomislav.ilicic120
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