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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!