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Calculate Genotype quality from the PL

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

next-gen alignment snp
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updated by Ram Ram • written by stat.1405 • stat.1405

1 answer

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

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updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

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

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updated by Ram Ram • written by stat.1405 • stat.1405

Missing parentheses

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

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updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

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