Filtering By Genotype

Is there any way of filtering my data using Genotypes. For e.g. i want all those locus & alleles that have a 0/0 or 0/1 or 1/1 value of Genotype.

Can you be more specific? There are many genootypes at each locus, so you’ll need to phrase this as an aggregation: e.g. you want loci that have ANY 1/1 genotype, or loci where ALL genotypes are 0/0, etc.

Yes i want all loci (with every data row also) where 0/0 is prrsent.

something like:

mt = mt.filter_rows(hl.agg.any(mt.GT.is_hom_ref()))

This is returning all rows with “NA” except “0/0”, but i want only “0/0”.

Can you explain this part? What NA?

I only want the ids with locus and alleles that have a genotype of 1/1. Please HELP

Something like this may be what you want: