Greetings,
We have developed a tool that converts VCF files into the latest FHIR Genomics format, available here: https://github.com/openelimu/VCF-2-FHIR
We currently translate simple variants, along with zygosity and phase relationships. We are working on enhancing the conversion to accommodate structural variants. We also anticipate a code update later this year once January 2019 ballot comments against the FHIR Genomics guide have been resolved and applied.
We tested the converter against VCF files obtained from the 1000 Genomes project. A full description of the software, along with source code, source VCF files, and corresponding FHIR Genomics reports (in XML and JSON) can be found on the github site.
We hope this resource will help foster genomics-EHR integration.
Just a note that the converter has been updated. Output is now conformant with the recently published HL7 FHIR Genomics Implementation Guide (http://hl7.org/fhir/uv/genomics-reporting/index.html)
Another update: converter has been moved to here: https://github.com/elimuinformatics/vcf2fhir