How to filter out variants overlapping with a deletion

Hail Query & hailctl
1

Hi,

In VCF, if a variant is overlapping with a deletion, the ALT field will have a * (e.g. ALT: T,*). since hail vds has a multi split step, I am wondering how to filter out such variants in hail syntax (both 0.1 and 0.2 version). Thanks.

2

Do you want to filter out the variant or the allele?

3

the variant, thanks.

4

in 0.2:

mt = mt.filter_rows(mt.alleles[1:].any(lambda aa: aa == '*'))
5

I don’t really remember how to do this in 0.1. It’s much harder there.