Error summary: HailException: Only support ploidy == 2 and unphased. Found 1|1

Hail Query & hailctl
1

Hi there,

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?

mt.annotate_entries(GT=hl.case()
.when(mt.GT.is_diploid(), hl.call(mt.GT[0], mt.GT[1], phased=False))
.when(mt.GT.is_haploid(), hl.call(mt.GT[0], phased=False))
.default(hl.null(hl.tcall)))

Many thanks,

2

That 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.

3

Hi Dan,

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.

Thanks

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