I want to do something very simple. I want to keep sites that do not have any missing genotypes (i.e. 100% present across all samples).
In vcftools I usually do
--max-missing 1.0 as indicated in the manual, but I want to use BCFTOOLS as it is much quicker. However, I cannot find the equivalent flag to do this. I have only found
F_MISSING, which I think removes individuals and not sites.