Output Reference¶
The ClinVar-GKS pipeline produces a single compressed JSON file per release, containing all variant representations, clinical classification statements, and supporting reference data. This section documents the output from a consumer perspective — how the file is structured, what each section contains, and how to interpret the data.
For details on how the output is built, see the Pipeline documentation.
Release Format¶
Each release is available as a gzip-compressed JSON file (.json.gz) containing a root-level object with bundle sections, and optionally as a set of typed Parquet files (one per section). Each bundle section is a keyed collection — the key is the object's unique identifier, and the value is the complete object.
See Output Format Overview for a detailed guide to the bundle structure, reference patterns, and how to navigate between sections.
Sections¶
| Section | Content | Key Format |
|---|---|---|
sequenceReference |
VRS sequence references | SQ.{digest} |
location |
VRS sequence locations | ga4gh:SL.{digest} |
allele |
VRS alleles with expressions | ga4gh:VA.{digest} |
copyNumberCount |
Copy number count variants | clinvar:{id} |
copyNumberChange |
Copy number change variants | clinvar:{id} |
gene |
Gene MappableConcepts | ncbigene:{id} |
variation |
Cat-VRS categorical variants | clinvar:{variation_id} |
condition |
Trait/disease concepts | clinvar.trait:{id} |
conditionSet |
Multi-condition groupings | clinvar.traitset:{id} |
submitter |
Submitting organizations | clinvar.submitter:{id} |
proposition |
Classification propositions | {scv_id}-{CODE} / {vcv_id}-{group}-{prop}-{level} |
evidenceLine |
Evidence lines (SCV, VCV, RCV) | {id}.contributing / {scv_id}.{ver} |
scv |
Submitted classifications | clinvar.submission:{scv_id}.{version} |
vcv |
Variation-level aggregates | {vcv_id}-{group}-{prop}-{level} |
rcv |
Condition-level aggregates | {rcv_id}-{group}-{prop}-{level} |
Format Conventions¶
- Null stripping — null-valued fields and empty arrays/objects are omitted from the output
- GA4GH identifiers — VRS identifiers use the
ga4gh:prefix (e.g.,ga4gh:VA.abc123) - ClinVar identifiers — ClinVar-scoped identifiers use the
clinvar:prefix (e.g.,clinvar:12345) - JSON pointer references — objects reference each other using
#/{section}/{key}strings (e.g.,#/allele/ga4gh:VA.abc123)
Cross-Section References¶
Objects reference each other using #/ JSON pointer strings rather than embedding full objects. This keeps the file compact and avoids duplication. For example:
- A variation references its allele as
#/allele/ga4gh:VA.abc123 - An SCV statement references its proposition as
#/proposition/SCV001234567-PATH - A VCV evidence line references its contributing SCVs as
#/scv/clinvar.submission:SCV001234567.1
See ID References for the complete reference format guide, identifier patterns, and resolution rules.
Specifications¶
The output conforms to these GA4GH standards: