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  • samtools pileup base quality

    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!

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