Bio Variant Annotation
GPTomics/bioSkills
Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools annotate/csq, Ensembl VEP, SnpEff, and ANNOVAR.
Agent skill
Bio Variant Annotation
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR.
No licenceAuto-check passed
Install Bio Variant Annotation
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-annotation --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-variant-annotation .claude/skills/bio-variant-annotation && 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 "bio-variant-annotation" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotation into .claude/skills/bio-variant-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-annotation", 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/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotationType 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-annotation --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-variant-annotation .agents/skills/bio-variant-annotation && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-variant-annotation" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotation into .agents/skills/bio-variant-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-annotation", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-annotation --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-variant-annotation .cursor/skills/bio-variant-annotation && 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 "bio-variant-annotation" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotation into .cursor/skills/bio-variant-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-annotation", 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/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-variant-annotation--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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-annotation --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-variant-annotation .gemini/skills/bio-variant-annotation && 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 "bio-variant-annotation" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotation into .gemini/skills/bio-variant-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-annotation", 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 FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-annotationInstalls 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-variant-annotation .github/skills/bio-variant-annotation && 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 "bio-variant-annotation" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotation into .github/skills/bio-variant-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-annotation", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-annotation --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-variant-annotation .opencode/skills/bio-variant-annotation && 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 "bio-variant-annotation" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotation into .opencode/skills/bio-variant-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-annotation", 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
bio-variant-annotation- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2.9k tokens
- SKILL.md length
- 616 words
- Files
- 3
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR.
- Annotating variants with functional and clinical information
- SKILL.md covers Version Compatibility, Tool Comparison, bcftools annotate and bcftools csq, plus 3 more sections
- Runs Shell scripts from its folder; calls conda and pip; reaches annovar.openbioinformatics.org
What it does
Bio Variant Annotation is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.
Its SKILL.md is about 2.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/annotate_vcf.sh` and `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Annotating variants with functional and clinical information
Example prompts
- “/bio-variant-annotation”
Requirements
- Python 3
- A Bash shell
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. 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
Ships script files (Shell), which the agent can run.
Shell commands in SKILL.md call:
condapip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
annovar.openbioinformatics.org
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
Bio Variant Annotation loads about 2.9k tokens when it runs. Until then it costs about 69 tokens; SKILL.md has 616 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
Without a licence we can't republish the file, so here is its outline and opening line. It has 616 words (~2,919 tokens).
“Reference examples tested with: bcftools 1.19+”
- name
- bio-variant-annotation
- tool_type
- mixed
- primary_tool
- VEP
Files
SKILL.md and 2 other files in skills/bio-variant-annotation of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/annotate_vcf.sh
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Bio Variant Annotation 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 |
|---|---|---|---|---|---|---|
| Bio Variant Annotation this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.9k | Automated safety check: Pass | None | |
| Bio Variant AnnotationGPTomics/bioSkills | 1.2k | 1 repos | ~6.4k | Automated safety check: Pass | MIT | |
| Annotating Variantsmaziyarpanahi/openmed | 5.5k | — | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Snpeff Variant Annotationjaechang-hits/SciAgent-Skills | 370 | 1 repos | ~5.4k | Automated safety check: Pass | MIT | |
| Variant AnnotationClawBio/ClawBio | 1.2k | 1 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Variant Annotationaipoch/medical-research-skills | 2k | — | ~3.5k | Automated safety check: Pass | MIT |
Similar skills
Annotating Variants
maziyarpanahi/openmed
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and…
Snpeff Variant Annotation
jaechang-hits/SciAgent-Skills
Annotate and filter VCF variants with SnpEff and SnpSift. An agent skill from jaechang-hits/SciAgent-Skills.
Variant Annotation
ClawBio/ClawBio
Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
Variant Annotation
aipoch/medical-research-skills
Query and annotate gene variants from ClinVar and dbSNP databases.
Bio Genome Annotation Annotation Qc
GPTomics/bioSkills
Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic…
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Questions about Bio Variant Annotation
What does Bio Variant Annotation do?
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Bio Variant Annotation is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR.
When should I use Bio Variant Annotation?
Bio Variant Annotation fits situations like: annotating variants with functional and clinical information.
How do I install Bio Variant Annotation in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a claude-code`. Or copy the skill folder (skills/bio-variant-annotation in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-variant-annotation in your project. Claude Code loads it when a task matches its description.
How do I install Bio Variant Annotation in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a codex`. Or copy the skill folder (skills/bio-variant-annotation in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-variant-annotation in your project. Codex loads it when a task matches its description.
Can I use Bio Variant Annotation 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-annotation -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-variant-annotation, .gemini/skills/bio-variant-annotation, .github/skills/bio-variant-annotation and .opencode/skills/bio-variant-annotation in your project.
What does Bio Variant Annotation need to run?
Going by SKILL.md and its folder, Bio Variant Annotation needs a shell for the scripts in its folder and the command-line tools its instructions call (conda and pip). Our summary lists: Python 3; A Bash shell.
Does Bio Variant Annotation access the network?
SKILL.md names 1 domain. In commands or code: annovar.openbioinformatics.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.
Is Bio Variant Annotation 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 Bio Variant Annotation use?
No licence was found for Bio Variant Annotation or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Variant Annotation use?
About 2.9k tokens (SKILL.md is roughly 12k 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 Bio Variant Annotation?
Skills that share tags, products or a category with Bio Variant Annotation: Bio Variant Annotation (GPTomics/bioSkills, 1.2k stars), Annotating Variants (maziyarpanahi/openmed, 5.5k stars), Snpeff Variant Annotation (jaechang-hits/SciAgent-Skills, 370 stars) and Variant Annotation (ClawBio/ClawBio, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Variant Annotation?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.