Repartition and missing values in a MT file


#1

Hello,

Does the function mt.repartition() still exist?

I have this result :
Hail version: 0.2-29fbaeaf265e
Error summary: AssertionError: assertion failed

Also, I have a dataset with 219,154,452 variants and 1,886 samples theoretically. But I doubt that this is the real number of variants because this MT results form merging several VCFs files and taking a subsample.

Is there a function to see how many real variants I have / to see empty cases though colums in my MT file ?

Thanks

Ines


#2

What’s the full stack trace for that assertion error? That looks like a bug.

If you’re interested in filtering monomorphic variants, you can do something like:

mt = mt.filter_rows(hl.agg.fraction(mt.GT.is_hom_ref()) < 1)