Question: Calculate Genotype quality from the PL
0
gravatar for stat.1405
4.6 years ago by
stat.140520
uk
stat.140520 wrote:

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

 

snp alignment next-gen • 2.3k views
ADD COMMENTlink written 4.6 years ago by stat.140520
1
gravatar for Zev.Kronenberg
4.6 years ago by
United States
Zev.Kronenberg11k wrote:

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

ADD COMMENTlink written 4.6 years ago by Zev.Kronenberg11k
1

Good, chanhing 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 REPLYlink written 4.6 years ago by stat.140520

Missing parentheses

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

ADD REPLYlink written 4.6 years ago by Zev.Kronenberg11k
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