samtools pileup base quality

[swapna]

Hello,

I would like to understand the pileup base quality scores for SNPs.

For example, I have this SNP call at one of the positions
T to Y (which is C or T).
The read depth is 61.
The base quality column is
C$C$C$.$C$C$CCC..CC.CC..C.CCC.CC.CCCCCC.....,,,,,,......,.......,,,

I suppose in this case . probably means 'same as the original base', which would be 'T' in this case. But I don't understand what the , and $ stand for.

What is the best way to determine the relative proportion of each base in case of ambiguous SNPs?

Can I just calculate the number of reads with the individual calls?

In the other calls I have come across the following symbols which I need help to interpret.
$ , . ~ ^ CAPITAL_LETTERS small_letters

Is there a parameter I can use in pileup to give me a score for the individual calls? I did not find anything helpful in the manual.


Apologies in case this question has already been asked/answered in the past. It would be great if somebody could direct me to the right thread.

Thanks!