Delete Missing Genotypes

Hail Query & hailctl
#1

How can i remove sites with missing more than 10% of the genotypes? Like the --geno flag from Plink.

#2

Any updates?

#3

filter_rows is the way to remove sites. I’d do this:

mt = hl.variant_qc(mt)
mt = mt.filter_rows(mt.variant_qc.call_rate > 0.90)
1 Like
#4

Thanks alot