Fig. 1

vcf2fhir conversion. The vcf2fhir utility takes a VCF file as input and outputs a FHIR Genomics report in JSON format. A simplified conceptual representation of the FHIR report is shown here to illustrate the main components. (VCF is a text file. It contains meta-information lines (prefixed with ‘##’), a header line (prefixed with ‘#’), and tab-delimited data lines each containing information about a variant. The CHROM and POS fields indicate the location of the variant. REF indicates the reference allele while ALT indicates the alternate allele. FILTER indicates if the variant call has passed applied filters. INFO is a semicolon-separated series of fields that further characterize a variant. FORMAT is colon-separated list of fields that characterize the genotype. Fields defined in FORMAT are valued for each tested sample, such as the NA12878 sample shown. A FHIR Genomics report is represented as a FHIR Diagnostic Report that contains information about the patient, and a set of observations. Each observation in the FHIR Genomics report conforms to a defined FHIR Observation ‘profile’ that constrains the information conveyed. In particular, the report includes zero or more ‘region-studied’ observations, ‘variant’ observations, and ‘sequence-phase-relationship’ observations, which are described in the text)