Connect your whole-genome sequencing data to AI coding assistants via the Model Context Protocol (MCP).
Query personal VCF files — variants, genes, pharmacogenomics, GWAS traits, polygenic risk scores, and ClinVar pathogenicity — directly from your IDE using natural language. Supports trio analysis (patient + parents) for inheritance determination.
┌──────────────────────────────────────────────────────────────────────┐
│ IDE (Antigravity / Codex / Claude Code) Windows 11 │
│ ┌──────────────────────┐ ┌─────────────────────┐ ┌────────────┐ │
│ │ genechat-mcp │ │ opencravat-mcp │ │ pomera │ │
│ │ WSL2 → Ubuntu │ │ cloud SSE │ │ Windows │ │
│ │ LOCAL VCF queries │ │ REMOTE variant │ │ Python │ │
│ │ ClinVar, SnpEff, │ │ annotation (VEST, │ │ Notes, │ │
│ │ PGx, GWAS, PRS │ │ REVEL, gnomAD…) │ │ Search, │ │
│ │ │ │ │ │ AI Tools │ │
│ └──────┬───────────────┘ └─────────────────────┘ └────────────┘ │
│ │ │
│ ┌────▼────────────────────────┐ │
│ │ C:\Users\<user>\ │ │
│ │ genechat-data\ │ │
│ │ Mat\ *.vcf.gz │ │
│ │ Father\ *.vcf.gz │ │
│ │ Mother\ *.vcf.gz │ │
│ └─────────────────────────────┘ │
└──────────────────────────────────────────────────────────────────────┘
| Server | Runs | Data Stays | Purpose |
|---|---|---|---|
| genechat-mcp | WSL2 (local) | On your machine | Query VCFs — variants, genes, PGx, GWAS, PRS, ClinVar |
| opencravat-mcp | Cloud SSE | Variant coordinates sent to mcp.opencravat.org |
Deep annotation — VEST, REVEL, CADD, gnomAD |
| pomera | Windows (local) | On your machine | Cross-session notes, web search, AI research tools |
- Antigravity — JSON config (
mcp_config.json) - Codex — TOML config (
config.toml) - Claude Code — CLI / JSON / native SSE
Full instructions with copy-paste commands are in the linked guides below.
- Install WSL2 + Ubuntu + Miniforge + bio tools + GeneChat CLI → Installation
- Prepare VCFs from Nebula / Sequencing.com (bgzip, index, validate) → VCF Preparation
- Configure IDE — wire MCP servers, register genomes, install databases → IDE Configuration
- Run workflows — trio analysis, variant annotation, cross-session persistence → Workflows
- Troubleshoot → Troubleshooting
| # | Guide | Description |
|---|---|---|
| 0 | Setup Guide | Start here — overview, prerequisites, reading order |
| 1 | Installation | WSL2, Miniforge, bcftools, SnpEff, GeneChat CLI |
| 2 | VCF Preparation | Nebula / Sequencing.com formats, bgzip, contig handling |
| 3 | IDE Configuration | serve.sh, Antigravity / Codex / Claude Code configs, Pomera, genome registration |
| 4 | Workflows | Trio analysis skill, gene investigation, variant annotation, documentation patterns |
| 5 | Troubleshooting | Common errors, verification checklist, recovery procedures |
| Component | Minimum | Purpose |
|---|---|---|
| Windows 11 | with WSL2 | Host OS |
| Python | 3.10+ | Pomera MCP server |
| Node.js | v18+ | mcp-remote proxy, Pomera npm wrapper |
| RAM | 16 GB | SnpEff needs 8 GB heap |
| Disk | ~10 GB | VCFs + ClinVar/SnpEff/GWAS databases |
- genechat-mcp is fully local — your VCF data never leaves your machine
- opencravat-mcp sends variant coordinates (rsIDs, chr/pos) to
mcp.opencravat.org(KarchinLab, Johns Hopkins) — a research service with no HIPAA/BAA guarantees - pomera stores notes locally; web search and AI tools route through configured external providers
- Never include patient names, DOB, or identifiers in any external-facing tool call
See Privacy Considerations for full details.
This guide orchestrates these open-source tools — it does not contain their source code:
- GeneChat-MCP — natecostello/genechat-mcp (MIT)
- OpenCRAVAT-MCP — KarchinLab/oc-mcp
- Pomera AI Commander — npmjs.com/package/pomera-ai-commander
Found an issue or have a suggestion? Open an issue or submit a pull request.
This project is licensed under the MIT License.