I am dealing with a time-sensitive project. I split multiallelics using Hail and exported to bgen using the parallel=“header-by-shard”. I then attempted to merge all the shards by converting to pgen and then merging them using plink2 (which worked for a chromosome with no multiallelics). I am now getting the following error. I would greatly appreciate help on resolving this, as I need the data for a conference! Should I go through the pvar files and replace the “.” with the row above it?
Error: The biallelic variants with ID '.' at position 22:49242904 in
pgen_chr22/part-1085-56ffabbe-1c33-4c10-b7a2-21c3486c0724.pvar appear to be the
components of a 'split' multiallelic variant; if so, it must be 'joined' (with
e.g. "bcftools norm -m") before a correct merge can occur. If you are SURE that
your data does not contain any same-position same-ID variant groups that should
be joined, you can suppress this error with --multiallelics-already-joined.
I need to keep multiallelics split because I will be taking this Hail bgen output and piping it into Regenie, which does not work with non-split multiallelic variants. Thus using bcftools norm (and joining multiallelics) is not appropriate.