vcf2fhir- A New Tool to Convert VCF files into HL7 FHIR Format

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A new utility is developed to convert variant calling format (VCF) files into HL7 FHIR format for the purpose of genomics electronic health records (EHR) integration. This is known as vcf2fhir [1].

Fast healthcare interoperability resource (FHIR) is a data format and an application programming interface to exchange EHR. HL7 FHIR language is an emerging language for EHR interoperability. vcf2fhir utility converts VCF files into HL7 FHIR diagnostic report.

How does vcf2fhir work?

  • It takes the VCF file as input.
  • vcf2fhir converts each row in the VCF file into a corresponding FHIR-formatted variant.
  • These variants include MNVs, SNVs, Indels, zygosity, and phase relationship.
  • Users are allowed to input genome build (‘GRCh37’ or ‘GRCh38’), a conversion region, a studied region that includes genomic regions already studied, and a non-callable region that includes studied uncallable regions.

The source code of vcf2fhir is available on Github. The software is written in python and is platform-independent.

For further information, read here.


  1. Dolin, R.H., Gothi, S.R., Boxwala, A. et al. (2021). vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. BMC Bioinformatics 22, 104.
Tariq is founder of Bioinformatics Review and a professional Software Developer at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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