vcf2fhir

vcf2fhir converts Variant Call Format (VCF) files into HL7 Fast Healthcare Interoperability Resources (FHIR) Genomics Diagnostic Reports to enable integration of genomic variant data with electronic health records.

Key Features:

• Conversion Capability: Translates VCF-formatted variants into a FHIR Genomics Diagnostic Report representation.
• Variant Types Supported: Represents Single Nucleotide Variants (SNVs), Multi-Nucleotide Variants (MNVs), and Indels and encodes zygosity and phase relationships across autosomes, sex chromosomes, and mitochondrial DNA.
• Customizable Input Parameters: Accepts specification of genome build (GRCh37 or GRCh38), optional conversion region coordinates, studied regions, and non-callable regions to inform conversion context.
• Region-Specific Conversion: Limits conversion to specified genomic coordinates when a conversion region is provided.
• Enhanced Reporting: Emits region-studied observations in the FHIR output that indicate analyzed segments and identify uncallable portions within studied or conversion regions.

Scientific Applications:

• Clinical Decision Support: Enables integration of FHIR-formatted genomic variants into clinical decision support workflows such as the SMART Cancer Navigator.
• Precision Genomics Integration: Supports platforms that merge FHIR-formatted clinical and genomic data with knowledge bases for delivery of context-relevant genomic findings and recommendations into EHR systems.
• Standards Evaluation and Research: Facilitates experimentation with and evaluation of FHIR Genomics standards, supports case-study based assessments of genomic-EHR integration, and indicates the need for further clinical validation for real-world deployment.

Methodology:

The conversion translates each VCF row into a corresponding FHIR-formatted variant within a generated Genomics Diagnostic Report, encoding zygosity, phase relationships, studied regions, and non-callable region annotations.