query PL field with bcftools
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Entering edit mode
6.0 years ago
Yahan ▴ 390

Hi BioStars,

I'd like to find the highest PL value (posterior likelihood for each possible genotype) for each sample in my VCf file.

From the documentation, I know that you can do 

MAX(DP)

which will find you the highest genotype depth over all samples

Since the PL field has a value for each possible genotype (e.g. 0/0, 0/1 and 1/1 for a biallelic variant, so 3 PL values), this mechanism is not applicable here.

If for instance

PL=0.233,0,0.767

Then I want to find 0.767

Is this possible with bcftools v1.2?

Thanks for the input.

bcftools SNP query view • 1.7k views
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