Nhomalt_grpmax and nhomalt_grpmax_non_ukb sometimes overflow (~2 billion)

General
1

Sometimes the nhomalt field seem to “underflow” into a number of signed int max.

Here for example is the values for 1: 12,235 G/A for the fields nhomalt_grpmax and nhomalt_grpmax_non_ukb in the VCF files:

nhomalt_grpmax=2147483647;nhomalt_grpmax_non_ukb=2147483647;

https://gnomad.broadinstitute.org/variant/1-12235-G-A?dataset=gnomad_r4

It seems to be an issue limited to these fields and for specific variants.

2

Hi @gaberudy,

Thank you for reporting this! This is a known bug in v4.0 VCFs where int64 fields with missing values in the Hail Table were incorrectly set to the max int32 instead of staying missing. We’ve put in a fix and this will be resolved in our v4.1 release.

Best,
Mike