Converts VCF variants into HL7 V2 format that conform to the HL7 Lab Results Interface Implementation Guide.
- In scope are somatic and germline simple variants (SNVs, MNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA.
- Supports VCF file (text-based or bgzipped) and optionally tabix files for query.
- Supports genome build ('GRCh37' or 'GRCh38');
- Optionally supports a query region in the form of .bed or dictionary that indicates the region(s) to convert.
- Optionally supports inclusion of 'region-studied' observations that detail which portions of the conversion region were studied.
- Optionally supports clinical annotations (e.g. clinical significance, phenotype), supplied in a separate annotation file.