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.
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
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: