Comments (1)
rhdolin
commented on June 7, 2024
1
Hi @apaytuvi . Thanks for writing.
This first version of software focused on a direct translation from VCF to FHIR, with minimal supplemental annotations. We agree with the value of adding more annotations, and it's on the list of future enhancements.
As for where they should go, I think we should remain aligned with the HL7 Genomics Reporting Implementation Guide. In the latest build, you'll see that the variant observation includes an optional 'gene-studied' component. I'd also suggest taking a look at the diagnostic-implication profile as the slot to put the disease.
Just as an aside, the FHIR genomics workgroup has a discussion forum here.
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Related Issues (20)
- Installation succeeds; "import vcf2fhir" fails HOT 2
- Add support for multi-sample VCFs HOT 5
- Meet the GitHub community checklist for public repository HOT 5
- Update Documentation HOT 5
- Simplifying the code HOT 9
- To resolve Resource Warning : unclosed file HOT 32
- GitHub Action to build and publish Python package to PyPI HOT 3
- Resource Warning due to the PyVCF3 library HOT 1
- Add genomic source class to variant observations HOT 4
- Error when conversion region wasn't studied HOT 1
- Support vcf2fhir on windows !
- conversion between 0-based and 1-based coordinate systems
- Extract simple variants based on conversion region HOT 1
- Deploy vcf2fhir on the bioconda channel
- Setup Dependabot for dependency updates
- Add Support for clinical annotations
- genetic variant assessment should be 'absent' when GT=0/0 HOT 3
- Add badges in Readme for higher visibility of project
- Create and add Project logo
- Incorrect output when ALT is a multi-valued list
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