When running a bq_to_vcf command on data that has list values for genotype, e.g. [-1, -1] the densify_variants._densify_variants method will create a VariantCall object that defaults to using the MISSING_GENOTYPE_VALUE, which is set to -1. In vcf_parser.VariantCall.lt the genotypes are compared, so comparing a scalar value to a list value results in an exception being thrown.
When running a bq_to_vcf command on data that has list values for genotype, e.g. [-1, -1] the densify_variants._densify_variants method will create a VariantCall object that defaults to using the MISSING_GENOTYPE_VALUE, which is set to -1. In vcf_parser.VariantCall.lt the genotypes are compared, so comparing a scalar value to a list value results in an exception being thrown.