Skip to content

Known Issues

This page documents the current release status, data-coverage limitations, and transformation caveats of the ClinVar-GKM pipeline.

Release status

This is the first official release (1.0.0) of ClinVar-GKM, built on the finalized GKM (Genomic Knowledge Model) standards — VRS 2.1.1, Cat-VRS 1.1.1, VA-Spec 1.1.0, and GKM-Core 1.3.0. Earlier builds were release candidates that tracked these specifications while they were in ballot review; now that the standards are finalized, the 1.0 output validates against the released schemas.

Data coverage

Each release includes 100% of the Germline and Somatic submission (SCV) records from the corresponding ClinVar XML release, and their classification content is carried through without modification to what ClinVar provides. However, the pipeline does not yet extract 100% of every attribute and tertiary content:

  • Case-level and functional data — aggregate case values, grouped/individual case-level evidence, and functional-data (incl. MaveDB) submissions are not currently extracted.
  • Rarely-provided attributes — some attributes that ClinVar provides only occasionally and sparsely may also not yet be represented.

If data that exists in ClinVar is missing here and would be useful to you, it can be added to the Roadmap and prioritized by community demand — open or upvote a discussion in the Ideas category. Case-level / functional data are already tracked as roadmap items (case data, functional data).

Outdated example files

The annotated JSONC/JSON example files in the repository's examples/ directory (VCV, RCV, SCV, and Cat-VRS) currently reflect an earlier output shape and do not match what the pipeline now produces in the bundles. They predate the four-section proposition refactor and the va-spec 1.1.0 conformance updates — for example, classification/confidence/strength are shown in an older form rather than as MappableConcept structs, and propositions are shown inline rather than in the datatype-specific sections. Refreshing them from current output is tracked in issue #115. Until then, treat the published bundle (and DESCRIBE on the Parquet files) as the source of truth for output structure, not the example files.

Additional edge cases, transformation caveats, and specific limitations will be documented here as they are identified.