Calculate Genotype quality from the PL

Question

[stat.1405]

I have an output of the call variants, VCF format.

I do not have the genotype quality (GQ) which is in the Format section. I have just the likelihood of the genotype (PL).

So, How can I calculate the genotype given the likelihood PL.

for example GT:PL:DP 1/0:255,0,255:62 how can I get the GQ?

Thanks

Answer 1

[Zev.Kronenberg]

unphred(0) / (unphred(0) + unphred(255) + unphred(255)). You example isn't ideal as it is pretty as perfect as a call gets.

[stat.1405]

Good, changing from phred score to unphred is 10^(-Q/10)

10^(-0/10)/10^(-0/10)+10^(-255/10)+10^(-255/10) = GQ is this correct

[Zev.Kronenberg]

Missing parentheses

fraction(best score)(sum of unphred all scores)