if this is the quality score Q= -10 log (P)
when P is the probability that the variant is wrong. or the call is wrong.if P =0.01 then the Q=20, P=0.001 then Q=30 and so on.
the question is :
1-. how they calculate P?
I read this paper to understand the calculation of P but its complicated.
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stat.1405 •
log() is log10() here (I realize that this is ambiguous), so it's just simple algebra.
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Devon Ryan
for (2), I did arrived to that -Q/10= logP, then I cannot make it as what is
should be e^Q/10=P
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stat.1405 •
Yeah, it's unfortunate that log() is such a common function but also has an ambiguous base. Sometimes it's log10() (like here), other times it's ln(), still other times it's log2() (I'm sure some group uses yet another base).
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Devon Ryan
Also, you forgot a negative sign
-10*log10(P)
^
As simple as this problem is there are plenty of gotchas. First the Phred Score was originally defined to quantify error, not correctness. In other words a high Phred score means there is a low chance of error. Widely used programs (not to be named) Phred scale probabilities of something being correct. Ask yourself when un-Phreding: Is the probability representing correctness or incorrectness.
The probability of the base or genotype being incorrectly called can be computed by:
10^(-phredScore/10)
Drop a couple of these lines into [R] to prove the correctness of the equation:
10^(-10/10) = 0.1 probability of error
10^(-20/10) = 0.01 probability of error
10^(-50/10) = 1e-5 probability of error
Summing it up watch our for Phred Scaled Likelihoods. They are not Phred Scores.
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Zev.Kronenberg
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