Using CombineVariants to update GT fields with phasing information

Hi GATK Team

I was wondering whether you guys have developed capability for updating GT fields with phasing information contained in another VCF? For instance, I generated phased genotypes using Beagle, and now simply want to update the genotype format fields of the unphased VCF (containing valuable FORMAT annotations that are lost after using Beagle). So I want to keep annotations and phasing information in one VCF.

I tried to do this using CombineVariants (Prioritize), however this only output the FORMAT fields of the prioritized vcf, rather than just merging them.

I realize you provide limited support to VCFs processed by non-GATK tools, but it would be helpful to know whether there is such capability that I am missing in the documentation.

Thanks for all your help!