If I may ask a bonus question, is there a way to perform the variant_qc with GP, by applying some threshold for the GP value maybe, or does Hail requires the GT field to be set?

The variant_qc function looks at the schema and generates a set of statistics using known fields (GT, DP, GQ, etc). But all its functionality can be expressed using annotate_rows and various aggregators.

I’m mostly interested in AC (for major and minor allele), AN, n_het, het_freq_hwe, and p_value_hwe, which are all given by variant_qc, but I get ValueError: 'variant_qc': expect an entry field 'GT' of type 'call' I’m guessing because I only have the GP field.

OK, the best thing to do then is to use annotate_entries to add a GT field computed from the GP using your definition. Then you can use variant_qc/sample_qc without any trouble.