I’m new to hail. I might have some very basic questions.
Currently, I am doing the genotype QC, to exclude chromosome Y for female participants. However, I was able to do is to either filter the matrix table to female participants only,
mt_female = mt.filter_cols(mt.pheno.is_female)
Or to use hl.filter_intervals to remove chrY for both male and female participants,
intervals = [hl.parse_locus_interval(x, reference_genome = ‘GRCh38’) for x in ‘chrY’]
mt_filtered = hl.filter_intervals(mt, intervals, keep = False)
Is it possible to remove chromosome Y from female participants?