Question: VCFtools filter missing genotypes conditional on a factor (population, species, etc.)
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gravatar for beausoleilmo
2.1 years ago by
beausoleilmo230
McGill University
beausoleilmo230 wrote:

I wonder if it's possible to filter missing genotype values with VCFtools conditional on a factor. As you can see on VCFtools website:

GENOTYPE VALUE FILTERING

--max-missing <float>

But I have a file that contains individuals coming from different populations. I would like to filter missing genotypes per population. As you can see in this image, the titles circled in red are the individuals. The last 3 letters (ful and for) are the species name. I would like this top be my conditional factor.

If VCFtools is not able to do this, how can I execute this?

enter image description here

vcftools ngs filter rad • 901 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by beausoleilmo230
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