VCFtools filter missing genotypes conditional on a factor (population, species, etc.)
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5.4 years ago
beausoleilmo ▴ 440

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 Filter NGS RAD • 2.0k views
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