SQL Optimization Patterns
ynulihao/AgentSkillOS
Master SQL query optimization, indexing strategies, and EXPLAIN analysis to dramatically improve database performance and eliminate slow queries.
Agent skill
Bio Variant Normalization
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Normalize indel representation and split multiallelic variants using bcftools norm.
Install Bio Variant Normalization
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-normalization -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-normalization --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-normalization .claude/skills/bio-variant-normalization && 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-normalization" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-normalization into .claude/skills/bio-variant-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-normalization", 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-normalizationType 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-normalization -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-normalization --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-normalization .agents/skills/bio-variant-normalization && 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-normalization" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-normalization into .agents/skills/bio-variant-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-normalization", 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-normalization -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-normalization --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-normalization .cursor/skills/bio-variant-normalization && 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-normalization" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-normalization into .cursor/skills/bio-variant-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-normalization", 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-normalization--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-normalization -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-variant-normalization --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-normalization .gemini/skills/bio-variant-normalization && 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-normalization" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-normalization into .gemini/skills/bio-variant-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-normalization", 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-normalizationInstalls 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-normalization -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-normalization .github/skills/bio-variant-normalization && 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-normalization" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-normalization into .github/skills/bio-variant-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-normalization", 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-normalization -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-normalization --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-normalization .opencode/skills/bio-variant-normalization && 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-normalization" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-normalization into .opencode/skills/bio-variant-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-variant-normalization", 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-normalization- GitHub stars
- 3.1k
- Token cost
- ~2.1k tokens
- SKILL.md length
- 609 words
- Files
- 3
- Skills in repo
- 173
- Repo updated
- First seen
- Licence
- None found
At a glance
Normalize indel representation and split multiallelic variants using bcftools norm.
- Works in 2 steps: Left-aligns indels → Splits multiallelic sites
- Comparing variants from different callers
- SKILL.md covers Version Compatibility, Why Normalize?, bcftools norm and Multiallelic Sites, plus 7 more sections
- Runs Shell scripts from its folder; calls pip
What it does
Bio Variant Normalization is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.
Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/normalize_vcf.sh` and `usage-guide.md`).
It sits in Databases, covering Database schema design. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Comparing variants from different callers
- Preparing VCF for downstream analysis
Example prompts
- “/bio-variant-normalization”
Requirements
- Python 3
- A Bash shell
Workflow steps
2 steps, taken from the first numbered list in SKILL.md.
- Left-aligns indels
- Splits multiallelic sites
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:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
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 Normalization loads about 2.1k tokens when it runs. Until then it costs about 51 tokens; SKILL.md has 609 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 609 words (~2,093 tokens).
“Reference examples tested with: bcftools 1.19+”
- name
- bio-variant-normalization
- tool_type
- cli
- primary_tool
- bcftools
Files
SKILL.md and 2 other files in skills/bio-variant-normalization of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/normalize_vcf.sh
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Compare with similar skills
Bio Variant Normalization 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 Normalization this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~2.1k | Automated safety check: Pass | None | |
| SQL Optimization Patternsynulihao/AgentSkillOS | 617 | 10 repos | ~3.3k | Automated safety check: Pass | None | |
| Add Mpk Taskmirage-project/mirage | 2.5k | — | ~4.5k | Automated safety check: Pass | Apache-2.0 | |
| B200 Flash Attention4 Plannermirage-project/mirage | 2.5k | — | ~1.9k | Automated safety check: Pass | Apache-2.0 | |
| Experiment Auditwanshuiyin/Auto-claude-code-research-in-sleep | 17k | 1 repos | ~2.7k | Automated safety check: Notes | MIT | |
| Datamodellmnimbalyst/nimbalyst | 1.8k | — | ~713 | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Bio Variant Normalization
What does Bio Variant Normalization do?
Normalize indel representation and split multiallelic variants using bcftools norm. Bio Variant Normalization is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Normalize indel representation and split multiallelic variants using bcftools norm.
When should I use Bio Variant Normalization?
Bio Variant Normalization fits situations like: comparing variants from different callers; preparing VCF for downstream analysis.
How do I install Bio Variant Normalization in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-normalization -a claude-code`. Or copy the skill folder (skills/bio-variant-normalization in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-variant-normalization in your project. Claude Code loads it when a task matches its description.
How do I install Bio Variant Normalization in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-normalization -a codex`. Or copy the skill folder (skills/bio-variant-normalization in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-variant-normalization in your project. Codex loads it when a task matches its description.
Can I use Bio Variant Normalization 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-normalization -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-normalization, .gemini/skills/bio-variant-normalization, .github/skills/bio-variant-normalization and .opencode/skills/bio-variant-normalization in your project.
What does Bio Variant Normalization need to run?
Going by SKILL.md and its folder, Bio Variant Normalization needs a shell for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3; A Bash shell.
Does Bio Variant Normalization access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Variant Normalization 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 Normalization use?
No licence was found for Bio Variant Normalization or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Variant Normalization use?
About 2.1k tokens (SKILL.md is roughly 8.4k 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 Bio Variant Normalization?
Skills that share tags, products or a category with Bio Variant Normalization: SQL Optimization Patterns (ynulihao/AgentSkillOS, 617 stars), Add Mpk Task (mirage-project/mirage, 2.5k stars), B200 Flash Attention4 Planner (mirage-project/mirage, 2.5k stars) and Experiment Audit (wanshuiyin/Auto-claude-code-research-in-sleep, 17k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Variant Normalization?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,051 GitHub stars. The repository holds 173 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.