I am running hail locally and get the following error after using .union_cols() to merge two files:
HailException: RVD error! Keys found out of order:
Current key: [1:49861205,[A,AGTGT]]
Previous key: [1:49861205,[A,AGTGTGTGT]]
This error can occur after a split_multi if the dataset
contains both multiallelic variants and duplicated loci.
I have run hl.split_multi_hts() on both files but now get it when I try to run pca, as well as the following which ran fine prior to the merge:
n = mt.count()
I have attempted to subsequently filter out split alleles using “mt.was_split == True, keep = False” to see if that helps but no luck so far. I’m a new user of hail so any help is much appreciated. Thanks in advance!