Question

Calculate Genotype quality from the PL

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9.5 years ago

stat.1405 ▴ 30

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 • 4.4k views

ADD COMMENT • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by stat.1405 ▴ 30

Ram · Answer 1 · 2014-10-14

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9.5 years ago

Zev.Kronenberg 12k

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

ADD COMMENT • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by Zev.Kronenberg 12k

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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

ADD REPLY • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by stat.1405 ▴ 30

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Missing parentheses

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

ADD REPLY • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by Zev.Kronenberg 12k