Don't trust the GT field. Check the reads.

A VCF's genotype field (GT) is the caller's conclusion, not the evidence. I had two "homozygous" candidates collapse when I looked at the reads. One was called 1/1 even though 34% of its reads carried the reference allele, so it was really a heterozygote. The false call had survived Franklin, gnomAD, MetaDome, AlphaFold, and an independent re-call, because none of those tools look at reads.