Mean impute missing genotypes

Hail Query & hailctl
1

Hi
Hail newbie here. What would be the best to mean impute missing genotypes?

Thank you

2

Good question, sorry we missed it.

So what I’d do is first get the mean of the each row. Assuming you have a matrix table mt, it’s:

mt = mt.annotate_entries(n_alt_alleles=mt.GT.n_alt_alleles())
mt = mt.annotate_rows(mean_gt = hl.agg.mean(mt.n_alt_alleles))

Now you want to fill in any missing values of n_alt_alleles with the mean you computed:

mt = mt.annotate_entries(n_alt_alleles=hl.coalesce(mt.n_alt_alleles, mt.mean_gt)

coalesce is a function that returns its first non-missing argument.

This gives you the mean number of alternate alleles for each geneotype. Let me know if that’s what you were looking for.