Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Build and inspect ClinVar exact-match evidence and candidate inventories.
Install Clinvar
$ npx skills add exon-research/genomi --skill clinvar -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install exon-research/genomi clinvar --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/clinvar .claude/skills/clinvar && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "clinvar" agent skill from https://github.com/exon-research/genomi/tree/master/skills/clinvar into .claude/skills/clinvar/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinvar", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/exon-research/genomi/tree/master/skills/clinvarType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add exon-research/genomi --skill clinvar -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install exon-research/genomi clinvar --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/clinvar .agents/skills/clinvar && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "clinvar" agent skill from https://github.com/exon-research/genomi/tree/master/skills/clinvar into .agents/skills/clinvar/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinvar", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add exon-research/genomi --skill clinvar -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install exon-research/genomi clinvar --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/clinvar .cursor/skills/clinvar && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "clinvar" agent skill from https://github.com/exon-research/genomi/tree/master/skills/clinvar into .cursor/skills/clinvar/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinvar", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/exon-research/genomi.git --path skills/clinvar--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add exon-research/genomi --skill clinvar -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install exon-research/genomi clinvar --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/clinvar .gemini/skills/clinvar && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "clinvar" agent skill from https://github.com/exon-research/genomi/tree/master/skills/clinvar into .gemini/skills/clinvar/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinvar", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install exon-research/genomi clinvarInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add exon-research/genomi --skill clinvar -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/clinvar .github/skills/clinvar && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "clinvar" agent skill from https://github.com/exon-research/genomi/tree/master/skills/clinvar into .github/skills/clinvar/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinvar", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add exon-research/genomi --skill clinvar -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install exon-research/genomi clinvar --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/clinvar .opencode/skills/clinvar && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "clinvar" agent skill from https://github.com/exon-research/genomi/tree/master/skills/clinvar into .opencode/skills/clinvar/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinvar", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
clinvar- GitHub stars
- 484
- Token cost
- ~1.1k tokens
- SKILL.md length
- 467 words
- Files
- 1
- Skills in repo
- 20
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Build and inspect ClinVar exact-match evidence and candidate inventories.
- Clinical labels
- SKILL.md covers Goal, Contract, Cross-Capability Synthesis and Tools, plus 2 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Carrier context
What it does
Clinvar is an agent skill from exon-research/genomi. Build and inspect ClinVar exact-match evidence and candidate inventories. Use for clinical labels, VUS/conflict, carrier context, and drug-response rows.
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science. The repository describes itself as: Local-first, open-source Claude Science alternative, before Claude Science is a thing. Turn your AI agent into personal DNA expert. The licence is Apache-2.0.
When your agent uses it
- Clinical labels
- Carrier context
- Drug-response rows
Example prompts
- “/clinvar”
What it can do on your machine
Read from SKILL.md and the folder at commit 1df4f5b. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Clinvar loads about 1.1k tokens when it runs. Until then it costs about 40 tokens; SKILL.md has 467 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from exon-research/genomi at commit 1df4f5b, republished under its Apache-2.0 licence (© exon-research). 467 words, ~1,102 tokens.
Download SKILL.mdSave it as
.claude/skills/clinvar/SKILL.md (or your agent's skills folder).- name
- clinvar
- description
- Build and inspect ClinVar exact-match evidence and candidate inventories. Use for clinical labels, VUS/conflict, carrier context, and drug-response rows.
- tools
- genomi.check_libraries, clinvar.match_variants, clinvar.scan_candidates, variant.gather_allele_context, variant.gather_gene_context
- mutating
- true
ClinVar Evidence
Use this skill when the user asks about clinical labels, carrier findings, pathogenic/likely pathogenic entries, VUS, conflicting classifications, drug response, risk-factor labels, or ClinVar-derived discovery.
Goal
Build a candidate landscape from exact ClinVar matches. Use
candidate_inventory as variant-level provenance evidence and
candidate_review_groups as the carrier/condition review inventory.
Convention: See
skills/conventions/evidence-quality.md.
Contract
- ClinVar matches provide exact/static evidence for source-backed interpretation.
- Exact matching requires the optional build-specific library
clinvar-grch38orclinvar-grch37. - Candidate inventories are variant-level evidence, not interpretation.
- Candidate review groups are review targets. A heterozygous P/LP group can be carrier-relevance evidence; it is not a carrier-status conclusion.
clinvar.scan_candidatesreturns an evidence view, grouped support, warnings, and coverage; use those fields rather than inferring priority from prose.- By default,
clinvar.scan_candidatesincludes P/LP, conflicting, VUS, risk/association/protective, drug-response, and benign ClinVar groups. - If ClinVar matches are missing,
clinvar.scan_candidatesmaterializes them from the Active Genome Index before building the candidate inventory. - VUS, conflicts, and low-review assertions are downgraded unless reviewed source evidence supports a stronger claim.
- Drug-response rows use pharmacogenomic source context before actionability is implied.
Cross-Capability Synthesis
A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.
Tools
clinvar.match_variants
Materialize exact ClinVar matches for comparable Active Genome Index variants using the installed build-specific ClinVar library.
Use when: After an Active Genome Index and the matching build-specific ClinVar library are available to materialize exact ClinVar/sample matches.
Why necessary: ClinVar matching is library-scoped materialization; it turns installed public ClinVar rows into exact matches for an Active Genome Index without forcing every genome-artifact task to run ClinVar.
Show full SKILL.md (188 more words)Show less
clinvar.scan_candidates
Build a deterministic candidate inventory and candidate review groups from exact ClinVar matches, materializing those matches from the Active Genome Index when needed.
Use when: Broad Active Genome Index disease or risk triage when exact ClinVar candidate inventory is needed.
Why necessary: Broad disease triage needs bounded ClinVar variant provenance plus review groups instead of ad hoc spot checks over a large genome file. It performs missing match materialization internally before candidate scanning.
Interpretation Rules
- Pathogenic/likely pathogenic labels need zygosity, inheritance, population frequency, gene-disease context, and source quality.
- Carrier language belongs in
phenotype.plan_risk_investigationwithinvestigation_type:"carrier_review"after reviewing the group gates. - VUS and conflicting labels use uncertainty/conflict wording.
- Drug-response labels require pharmacogenomic guideline context before clinical actionability is implied.
- Common association/risk/protective labels usually provide limited context for personal common-disease risk.
Routing Checks
- Prioritize ClinVar matches by actionability, review status, uncertainty, population context, inheritance, and zygosity.
- If a ClinVar operation returns
status="requires_library_install", explain how the named library helps this request and ask before installing it. - Treat ClinVar condition strings as database labels that need interpretation.
- Keep the whole candidate inventory local; send selected public targets to Journal source-review memory.
© exon-research, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/clinvar of exon-research/genomi.
Open the folder on GitHubat commit 1df4f5b
Compare with similar skills
Clinvar next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Clinvar this skillexon-research/genomi | 484 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Peer Reviewspacering-net/codeg | 3.9k | 17 repos | ~5.9k | Automated safety check: Notes | MIT |
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Related
Categories
Questions about Clinvar
What does Clinvar do?
Build and inspect ClinVar exact-match evidence and candidate inventories. Clinvar is an agent skill from exon-research/genomi. Build and inspect ClinVar exact-match evidence and candidate inventories.
When should I use Clinvar?
Clinvar fits situations like: clinical labels; carrier context; drug-response rows.
How do I install Clinvar in Claude Code?
Run `npx skills add exon-research/genomi --skill clinvar -a claude-code`. Or copy the skill folder (skills/clinvar in exon-research/genomi) into .claude/skills/clinvar in your project. Claude Code loads it when a task matches its description.
How do I install Clinvar in Codex?
Run `npx skills add exon-research/genomi --skill clinvar -a codex`. Or copy the skill folder (skills/clinvar in exon-research/genomi) into .agents/skills/clinvar in your project. Codex loads it when a task matches its description.
Can I use Clinvar in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add exon-research/genomi --skill clinvar -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/clinvar, .gemini/skills/clinvar, .github/skills/clinvar and .opencode/skills/clinvar in your project.
What does Clinvar need to run?
SKILL.md names no scripts, command-line tools or credentials: Clinvar is instructions for the agent only.
Does Clinvar access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Clinvar safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Clinvar use?
Clinvar is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Clinvar use?
About 1.1k tokens (SKILL.md is roughly 4.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Clinvar?
Skills that share tags, products or a category with Clinvar: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Clinvar?
exon-research (a GitHub organization) maintains it in exon-research/genomi, which has 484 GitHub stars. The repository holds 20 skills in this directory. The repository was last updated on August 31, 2026.
Source: exon-research/genomi on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.