Export only biallelic variants

Hail Query & hailctl
1

Hi all,

I used “hl.summarize_variants(data)” to get summary of my input. In this result, I am getting 2 alleles, 3 alleles and till 7 alleles. My question is there any option I can export only biallelic variants or triallelic variants?

2

If you want to remove variants that are multiallelic, try something like:

data = data.filter_rows(hl.len(data.alleles) < 3)

If you want to split multiallelics, take a look at split_multi_hts

3

Thank you @tpoterba