Hi - I have not been successful in using LD prune. Below is the code I am using.
b_mt = mt.filter_rows(hl.len(mt.alleles) == 2) t = b_mt.repartition(100) b_mt.write("repartitioned.mt", overwrite=True) r_mt = hl.read_matrix_table('repartitioned.mt') pruned_tbl = hl.ld_prune(r_mt.GT, r2 = 0.2, bp_window_size = 500000, block_size=75)
It takes a long time (hours) for a mt of ~1000 individuals having ~500,000 genotypes each.
I have tried various server configs but does not seem to help. Is there an example on LD pruning. My end goal is to find relatedness (king) within samples.
Any help is appreciated.