I first tried to reduce the block_size to 1024 as you suggested, which did not change the error message. I then tried to increase the subset of data (to appr a whole chromosome), now I get another Exception from running both ld_prune() and pc_relate():
“inbreeding does not support multiallelic variants/genotypes. Found genotype 0/2.”
I call split_multi() on the dataset first, as suggested by your guide. I assume this could create 0/2 genotypes, so I don’t understand the error.
I have added filter_rows(len(data.alleles) == 2) after the split_multi() call to be sure, but this returned the same exception.