Apologies for jumping into this discussion late. My question is what are the records in the intermediate VCF format? e.g. given two inputs

Truth

1 10 AT GT,AC 0/1

Query

1 10 A G 0/1
1 11 T C 0/1

What does the intermediate output look like for this matching case?

And for this non-matching case:

Truth

1 10 AT GT,AC 0/1

Query

1 10 A G 1/1
1 11 T C 1/1