Having some trouble running ld_prune. It doesn’t complete (seems to get stuck at some point).
This is what I’m currently running:
pruned_variant_ht = hl.ld_prune(ukb_gt_filtered_mt.GT, r2=0.9, bp_window_size=1000000, block_size=2048)
ukb_gwas_filtered_mt = ukb_gwas_filtered_mt.semi_join_rows(pruned_variant_ht)