We do this for technical reasons, mostly because we don't genotype in the HC anymore; it's all
done downstream by GenotypeGVCFs so we can't be sure that the genotype will be hom var. Also,
there are steps in the downstream pipeline where genotypes can change, so assuming anything in
the HC is a bad idea, and if we have phasing info in the het state, we want to propagate that forward.
Now, PGT tag fixing happens downstream in GenotypeGVCFs.
While I was in there I also cleaned up the code a bit and fixed a bug where annotation was happening
before genotype creation when using the --includeNonVariantSites argument.
Added tests accordingly.
5b087c9897