I am getting the following error:
> Hail version: 0.2.39-ef87446bd1c7
> Error summary: HailException: Only support ploidy == 2 and unphased. Found 1|1.
I was previously provided the code below to ‘hide’ the phased info, but it is currently not working as I am getting the above error after I execute it. Is there something I am missing?
.when(mt.GT.is_diploid(), hl.call(mt.GT, mt.GT, phased=False))
.when(mt.GT.is_haploid(), hl.call(mt.GT, phased=False))
annotate_entries is the right thing. Are you re-assigning the result to
mt, like this:
mt = mt.annotate_entries(...)
If yes, can you share the log file and the script? It’s possible you’ve found a Hail bug.
I am using mt =, yes, what I needed to do was re-impute the dataset to update the GT fields and that’s done the trick.