GWASos DomainOS¶

Status: Production
Engine: gwas-os
Domain: Statistical genetics (GWAS + post-GWAS + fine-mapping + PRS)

Statistical-genetics DomainOS covering association testing, fine-mapping, PRS construction, and locus-zoom visualization. Post-GWAS steps enrich loci with Open Targets drug-target context and ChEMBL bioactivity.

Field	Value
Product	GWASos
Engine id	`gwas-os`
Intent key	`gwas_os`
Repository	`Hordago-Labs/GWASos`
Plugin	`gwas-os`
Maturity (registry)	Production

Overview¶

Statistical-genetics DomainOS covering association testing, fine-mapping, PRS construction, and locus-zoom visualization. Post-GWAS steps enrich loci with Open Targets drug-target context and ChEMBL bioactivity.

Scientific approach¶

GWASos structures every run as 5 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.

#	Phase	Gate	HITL
1	QC & Harmonization	Confirm cohort QC and allele harmonization.	No
2	Association Testing	Run association model, inspect lambda/QQ.	No
3	Fine-Mapping	Resolve credible sets at genome-wide loci.	No
4	Post-GWAS Enrichment	Attach drug-target and bioactivity context.	No
5	PRS Construction	Approve PRS model and ancestry scope.	Yes

Capabilities & evidence objects¶

Domain tools / skills

association-test
fine-mapping
locus-zoom
prs-construction

Evidence objects

Object	Role	Consumer
`result.json`	produces	co-writer / hordago-dataviz (locus zoom)
`provenance.json`	produces	evidence-audit

Canonical artifacts (5-artifact contract)

Planned

The 5-artifact contract below is the target shape. Canonical-artifact emission is tracked as inherited debt (Wave 3C) and is not yet guaranteed.

Artifact	Description
`result.json`	Structured primary result payload for the domain run.
`report.md`	Human-readable narrative summary of the analysis.
`provenance.json`	Tool versions, reference data, and algorithm lineage for reproducibility.
`gate_status.json`	Per-phase gate pass/fail decisions.
`session_summary.json`	Session metadata for replay and audit.

Standalone quickstart¶

Zero platform dependency

This quickstart runs the DomainOS standalone. The Hordago platform is not required; platform composition is opt-in (see Composition below).

Install the standalone gwas-os plugin (Hordago-Labs/GWASos) -- no Hordago platform required.
Invoke the domain skill with a GWASos intent (see the intent keywords below).
Review the emitted artifacts under the run's output directory.

Intent keywords (route to this engine):

gwasos gwas.?os\b gwas pipeline gwas workflow gwas-os post-gwas locus zoom validated gwas

Worked example¶

Post-GWAS locus zoom with drug-target context

A user runs a GWAS fine-mapping study. After association testing and credible-set resolution, GWASos enriches the lead locus with Open Targets evidence and renders a locus-zoom figure, then proposes a PRS model gated on ancestry scope.

Validation & benchmarks¶

Benchmarks

Genomic-control lambda calibration
Credible-set coverage checks

Reproducibility. provenance.json pins reference panel and summary-statistic harmonization steps.

Reference¶

MCP fallback servers (used when the plugin is unavailable): pubmed, open-targets, chembl

Source documents

GWASos integration: references/gwasos-integration.md
GWAS wrapper PoC: references/gwas-wrapper-poc.md

Composition¶

Platform opt-in

GWASos runs standalone. When composed under the Hordago platform it gains cross-domain routing, the Shared Compiler gate, and evidence-audit provenance enforcement. Platform composition is opt-in; the quickstart above has zero platform dependency.

Cross-domain dependencies

Engine	Relationship
`prs-os`	Explicit PRS-tool phrasing (LDpred/PRSice) routes to prs-os; generic 'polygenic' stays on GWASos.
`onco-os`	Shares Open Targets / ChEMBL post-GWAS enrichment MCPs.