Unfortunately our support for malformed VCFs is pretty bad – we don’t have a way to skip failing lines, etc. This is a terrible error message, though, and needs to print the offending field. I’ve made an issue to track it (https://github.com/hail-is/hail/issues/2232).
I think the best thing to do right now is to reheader the VCF fixing the header line for the problematic INFO field. Probably the necessary fix is to change the
Number of some field from
When we’ve fixed the error message, this should be a bit easier to see what’s going on. For now, though, you can grep for
0,0 in the INFO field of the variant printed.