Research Demo Variant Review Workbench
Research-use only. This hosted interface demonstrates the pipeline and reporting workflow. It is not a clinical system, privacy boundary, or PHI-ready platform.

Project Overview

Variant Review Workbench

This web interface sits on top of the existing CLI-first architecture. The shared pipeline remains responsible for ClinVar matching, conflict surfacing, optional PharmGKB enrichment, ranking, reporting, and export generation.

Open the run form View repository
What this app is

A browser entry point for the same research pipeline and output contract already used by the CLI.

What it demonstrates

Reusable backend orchestration, artifact provenance, a hosted report workflow, and deployment-aware runtime controls.

What it is not

A clinical decision system, diagnostic portal, or privacy boundary for patient-identifying data.

Browser workflow

  • Upload a validated `.vcf` or `.vcf.gz` file.
  • Select the matching assembly: `GRCh37` or `GRCh38`.
  • Optionally enable PharmGKB enrichment for additional public PGx context.
  • Either open the report in the browser or redirect straight to HTML, JSON, or Markdown export.

Generated outputs

  • Embedded generated HTML report from the same report builder used by the CLI.
  • Export artifacts in HTML, JSON, and Markdown.
  • Machine-readable run status endpoint for polling.
  • Run-local artifact directories with reproducibility metadata and summary outputs.

The browser interface remains additive. The CLI is still the canonical execution path for local scripted use.

Hosted demo guardrails

  • Research-use only, with no clinical decision support claims.
  • Uploads are capped at 25 MB per request.
  • Submitted files are retained in run-local storage for roughly 24 hours, subject to cleanup timing.
  • Do not submit protected health information or production patient data.

Deployment notes

  • The mounted disk stores raw ClinVar inputs, temporary run workspaces, and a shared processed ClinVar cache.
  • The processed ClinVar cache should be built offline and uploaded before treating the hosted site as ready.
  • `/healthz` should be used only after required runtime paths and ClinVar inputs exist on disk.

ReadMe highlights

  • The repository includes both CLI and web quick-start paths.
  • The processed ClinVar cache is now documented as a reusable shared dependency, not a per-query warm-up.
  • `DEPLOYMENT.md` captures the Render disk layout, environment variables, and smoke-test workflow.

Why this matters

  • The hosted demo now communicates the same process as the repository docs.
  • Users are less likely to confuse run retention with cache build timing.
  • The web app presents itself as a serious review tool rather than an exploratory mockup.