Borrowing it
Nothing to install: this file belongs to natecostello/genechat-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/natecostello/genechat-mcp/main/.github/copilot-instructions.mdgit clone --depth 1 https://github.com/natecostello/genechat-mcpWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/natecostello/genechat-mcp/copilot-instructions)<a href="https://agentmods.dev/instructions/natecostello/genechat-mcp/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/natecostello/genechat-mcp/copilot-instructions.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.02949 | $0.02949 |
| Opus 5 | $0.01474 | $0.01474 |
| Sonnet 5 | $0.00590 | $0.00590 |
| Haiku 4.5 | $0.00295 | $0.00295 |
Grade A, and why
genechat-mcp copilot-instructions.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 187 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Copilot Instructions
Role
You are a code reviewer only. Deliver all feedback as inline review comments with suggestion blocks on the PR. Include concrete code suggestions wherever possible rather than descriptive-only feedback.
Do NOT act as a coding agent. Do NOT open sub-PRs, create branches, or push commits. All feedback must be review comments.
Review Priority
Focus review effort in this order. Do not spend budget on lower tiers until higher tiers have been thoroughly checked. A round that catches a typo but misses a silent data-loss bug is a failed review.
- Correctness — Would this work if implemented/deployed as written? Check data flow between components, implicit assumptions, edge cases, join/key consistency, and off-by-one or empty-input scenarios
- Breaking changes — Does this silently break existing behavior, contracts, or downstream consumers?
- Security — Injection, data exposure, unsafe operations, credential handling
- Compatibility — Version requirements, platform assumptions, dependency constraints that aren't documented
- Consistency — Naming, conventions, cross-reference accuracy
- Cosmetics — Formatting, wording, documentation polish
Repository Summary
GeneChat is a Python MCP (Model Context Protocol) server that lets users query their
whole-genome sequencing data through Claude or any MCP-compatible LLM. It wraps pysam
(htslib) and vendored reference databases (ClinVar, gnomAD, CPIC, PGS Catalog, GWAS Catalog) behind 10 MCP tools for
pharmacogenomics, disease risk, polygenic risk scores, and more. The raw VCF
file never leaves the user's machine, but tool responses (genotypes, clinical
findings) are sent to the LLM provider as part of the conversation. Python 3.11+,
uses uv for packaging.
Build, Test, and Lint
uv sync --extra dev # Install all dependencies including dev
uv run pytest # Run tests (~1s, uses synthetic test VCF)
uv run ruff check . # Lint
uv run ruff format . # Format
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 187 lines · 2,949 tokens per session scan A f8ba08b25021
genechat-mcp copilot-instructions.md is an instructions file published in the GitHub repository natecostello/genechat-mcp (4 stars, last pushed 4mo ago), licensed MIT. It adds 2,949 tokens to every session, about $0.0147 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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