Question: query PL field with bcftools
1
gravatar for Yahan
4.0 years ago by
Yahan370
Belgium
Yahan370 wrote:

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.

query snp view bcftools • 1.1k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Yahan370
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 574 users visited in the last hour