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).
BQithe same as
- And do you always have to subtract with 64
BQi -64or is it depended on the sequencer used?
I would really appreciate some help.