Thanks for the response, I’ll try this.
I should not have any missingness in the phenotypes as I filtered all of those out before creating the matrix table.
No worries, I’m relatively new to this analysis. I got that number from this thread.
I’m checking how many rows this loses. However, counting the rows on the geno matrix tables takes forever (eg geno_mt.count_rows(). I’m not sure if this is normal or not?