How to filter out variants overlapping with a deletion


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.

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

the variant, thanks.

in 0.2:

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

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