Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Agent skill
Bio Gatk Variant Calling
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Variant calling with GATK HaplotypeCaller following best practices.
Install Bio Gatk Variant Calling
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-gatk-variant-calling -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-gatk-variant-calling --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-gatk-variant-calling .claude/skills/bio-gatk-variant-calling && 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-gatk-variant-calling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-gatk-variant-calling into .claude/skills/bio-gatk-variant-calling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-gatk-variant-calling", 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-gatk-variant-callingType 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-gatk-variant-calling -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-gatk-variant-calling --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-gatk-variant-calling .agents/skills/bio-gatk-variant-calling && 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-gatk-variant-calling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-gatk-variant-calling into .agents/skills/bio-gatk-variant-calling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-gatk-variant-calling", 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-gatk-variant-calling -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-gatk-variant-calling --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-gatk-variant-calling .cursor/skills/bio-gatk-variant-calling && 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-gatk-variant-calling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-gatk-variant-calling into .cursor/skills/bio-gatk-variant-calling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-gatk-variant-calling", 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-gatk-variant-calling--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-gatk-variant-calling -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-gatk-variant-calling --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-gatk-variant-calling .gemini/skills/bio-gatk-variant-calling && 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-gatk-variant-calling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-gatk-variant-calling into .gemini/skills/bio-gatk-variant-calling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-gatk-variant-calling", 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-gatk-variant-callingInstalls 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-gatk-variant-calling -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-gatk-variant-calling .github/skills/bio-gatk-variant-calling && 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-gatk-variant-calling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-gatk-variant-calling into .github/skills/bio-gatk-variant-calling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-gatk-variant-calling", 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-gatk-variant-calling -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-gatk-variant-calling --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-gatk-variant-calling .opencode/skills/bio-gatk-variant-calling && 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-gatk-variant-calling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-gatk-variant-calling into .opencode/skills/bio-gatk-variant-calling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-gatk-variant-calling", 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-gatk-variant-calling- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2.8k tokens
- SKILL.md length
- 563 words
- Files
- 4
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Variant calling with GATK HaplotypeCaller following best practices.
- Works in 5 steps: Generate GVCFs per Sample → Combine GVCFs (GenomicsDBImport) → Joint Genotyping → …
- Calling variants with GATK HaplotypeCaller
- SKILL.md covers Version Compatibility, Prerequisites, Single-Sample Calling and GVCF Workflow (Recommended for…, plus 6 more sections
- Runs Shell scripts from its folder
What it does
Bio Gatk Variant Calling is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.
Its SKILL.md is about 2.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `examples/joint_calling.sh`, `examples/single_sample.sh` and `usage-guide.md`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Calling variants with GATK HaplotypeCaller
- Tasks that involve Bioinformatics
Example prompts
- “/bio-gatk-variant-calling”
Requirements
- A Bash shell
Workflow steps
5 steps, taken from the step headings in SKILL.md.
- Generate GVCFs per Sample
- Combine GVCFs (GenomicsDBImport)
- Joint Genotyping
- BaseRecalibrator
- ApplyBQSR
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.
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
Bio Gatk Variant Calling loads about 2.8k tokens when it runs. Until then it costs about 68 tokens; SKILL.md has 563 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 563 words (~2,816 tokens).
“Reference examples tested with: GATK 4.5+, bcftools 1.19+”
- name
- bio-gatk-variant-calling
- tool_type
- cli
- primary_tool
- gatk
Files
SKILL.md and 3 other files in skills/bio-gatk-variant-calling of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/joint_calling.sh
- examples/single_sample.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 9, 2026.
Compare with similar skills
Bio Gatk Variant Calling 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 Gatk Variant Calling this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.8k | Automated safety check: Pass | None | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Clinvar Database
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Metabolic Study Planner
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Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
MFA Pipeline Orchestrator
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Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
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Related
Categories
Questions about Bio Gatk Variant Calling
What does Bio Gatk Variant Calling do?
Variant calling with GATK HaplotypeCaller following best practices. Bio Gatk Variant Calling is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Variant calling with GATK HaplotypeCaller following best practices.
When should I use Bio Gatk Variant Calling?
Bio Gatk Variant Calling fits situations like: calling variants with GATK HaplotypeCaller; tasks that involve Bioinformatics.
How do I install Bio Gatk Variant Calling in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-gatk-variant-calling -a claude-code`. Or copy the skill folder (skills/bio-gatk-variant-calling in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-gatk-variant-calling in your project. Claude Code loads it when a task matches its description.
How do I install Bio Gatk Variant Calling in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-gatk-variant-calling -a codex`. Or copy the skill folder (skills/bio-gatk-variant-calling in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-gatk-variant-calling in your project. Codex loads it when a task matches its description.
Can I use Bio Gatk Variant Calling 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-gatk-variant-calling -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-gatk-variant-calling, .gemini/skills/bio-gatk-variant-calling, .github/skills/bio-gatk-variant-calling and .opencode/skills/bio-gatk-variant-calling in your project.
What does Bio Gatk Variant Calling need to run?
Going by SKILL.md and its folder, Bio Gatk Variant Calling needs a shell for the scripts in its folder. Our summary lists: A Bash shell.
Does Bio Gatk Variant Calling 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 Bio Gatk Variant Calling 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 Gatk Variant Calling use?
No licence was found for Bio Gatk Variant Calling or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Gatk Variant Calling use?
About 2.8k tokens (SKILL.md is roughly 11k 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 Gatk Variant Calling?
Skills that share tags, products or a category with Bio Gatk Variant Calling: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Gatk Variant Calling?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 GitHub stars. The repository holds 279 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.