ga4gh/va-spec

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An information model for representing variant annotations.

Stars: 27
Forks: 7
Open beginner issues: 0
Indexed issues: 119
Avg merge: 3m
Merged PRs (30d): 1

Dominant language: Jupyter Notebook
License: Apache-2.0
Last GitHub push: Aug 10, 2026
Latest indexed: Sep 16, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: help wanted

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119 open issues indexed

Feedback on Annotation-Statement cardinality Open

ga4gh/va-spec#1 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Generalize the 'Case-Control' Annotation Type Open

ga4gh/va-spec#2 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Delineate types of clinically significant variant-condition annotations Open

ga4gh/va-spec#3 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Molecular Consequence Annotation Definition and Scope Open

VA type definition

ga4gh/va-spec#4 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
'Allele' vs 'Variant' Open

ga4gh/va-spec#5 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Repo name consideration to stay in sync with var rep approach Open

ga4gh/va-spec#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Variant Pathogenicity definition clarification Open

ga4gh/va-spec#7 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Referencing/representing 'extra' variant info as metadata within an annotation Open

ga4gh/va-spec#8 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Classifying the Variant-Side Effect Annotation type Open

ga4gh/va-spec#9 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Relationship between 'Population Frequency', 'Relative Population Frequency', and 'Condition Risk' Annotations Open

ga4gh/va-spec#10 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Refining the qualifier paradigm in the Annotation Content Model Open

ga4gh/va-spec#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
types of variants we would ideally support Open

ga4gh/va-spec#13 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Feedback requested on spreadsheet format for defining Variant Annotation models Open

ga4gh/va-spec#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling 'Contributions' Open

ga4gh/va-spec#15 · 13 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Constraining annotation subject to transcript level variants for Molecular Consequence Open

ga4gh/va-spec#16 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
derived vs observed variant Open

ga4gh/va-spec#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Relative Location (Affected Feature) Annotation Definition and Scope Open

VA type definition

ga4gh/va-spec#18 · 19 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling of 'Sequence Feature' (as a Domain Entity) Open

domain entity

ga4gh/va-spec#19 · 13 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Degree of adherence to ACM in modeling and message structure Open

data modeling message structure

ga4gh/va-spec#20 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Predicted Functional Impact Annotation Definition and Scope Open

VA type definition

ga4gh/va-spec#21 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Variant Pathogenicity Interpretation definition and scope Open

VA type definition

ga4gh/va-spec#22 · 21 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Variant Oncogenicity Interpretation definition and scope Open

VA type definition

ga4gh/va-spec#23 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling 'Genetic Condition' (as a Domain Entity) Open

domain entity

ga4gh/va-spec#24 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Capturing unspecified conditions in Variant Pathogenicity Interpretations Open

ga4gh/va-spec#25 · 19 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Variant origin terms Open

ga4gh/va-spec#26 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Competency Questions for Evidence/Provenance Modeling Open

ga4gh/va-spec#27 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Oncogenicity mechanism value set Open

ga4gh/va-spec#28 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Clarify the semantics of Oncogenicity vs Pathogenicity Open

ga4gh/va-spec#29 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Consider an allelic requirement qualifier on Variant Pathogenicity Interpretations Open

ga4gh/va-spec#30 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Therapeutic Response Annotation Definition and Scope Open

VA type definition

ga4gh/va-spec#31 · 28 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling 'Therapeutic Intervention' (as a Domain Entity) Open

domain entity

ga4gh/va-spec#32 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Names and values for Therapeutic Response 'predicates' Open

ga4gh/va-spec#33 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Experimental Functional Impact Annotation Definition and Scope Open

VA type definition

ga4gh/va-spec#34 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Funtional Impact Prediction Tool Review Open

ga4gh/va-spec#35 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Names for high-level Variation categories Open

ga4gh/va-spec#36 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Name for 'Variation Equivalence Set' concept Open

ga4gh/va-spec#37 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Population Frequency Annotation Definition and Scope Open

VA type definition

ga4gh/va-spec#38 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling 'Population' (as a Domain Entity) Open

domain entity

ga4gh/va-spec#39 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling 'Study Data' as containers for data items Open

domain entity

ga4gh/va-spec#40 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
General thoughts on Principle vs Pragmatism Open

ga4gh/va-spec#41 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Extend Population Frequency Annotation to cover MAF/FAF? Open

ga4gh/va-spec#42 · 11 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Provenance for sequencing data in PopFreq Annotations Open

ga4gh/va-spec#43 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Consider allowing 'ref' allele as qualifier on VA statements Open

ga4gh/va-spec#44 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Separating PopFreq annotations based on exome vs genome sequencing Open

ga4gh/va-spec#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Variant-Level Metadata object proposal Open

ga4gh/va-spec#46 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Meaning of the 'variant origin' qualifier Open

ga4gh/va-spec#47 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
An "Aggregate Clinical Significance Statement" for VCVs/RCVs Open

VA type definition

ga4gh/va-spec#48 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Representing different levels of provenance for 'informational entities' Open

ga4gh/va-spec#49 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Utility of the VA object Open

ga4gh/va-spec#50 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Modeling metadata for 'static' Variation Sets Open

ga4gh/va-spec#51 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026

ga4gh/va-spec

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