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Agent skill

Bio Copy Number Gatk Cnv

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Call copy number variants using GATK best practices workflow.

No licenceAuto-check passed

Install Bio Copy Number Gatk Cnv

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-gatk-cnv -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-copy-number-gatk-cnv --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-copy-number-gatk-cnv .claude/skills/bio-copy-number-gatk-cnv && rm -rf skills-src

Use ~/.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/

Facts

Skill name
bio-copy-number-gatk-cnv
GitHub stars
3.1k
Token cost
~2.1k tokens
SKILL.md length
379 words
Files
3
Skills in repo
279
Repo updated
First seen
Licence
None found

At a glance

Call copy number variants using GATK best practices workflow.

  • Works in 7 steps: Preprocess Intervals → Collect Read Counts → Create Panel of Normals → …
  • Following GATK best practices
  • SKILL.md covers Version Compatibility, Somatic CNV Workflow Overview, Step 1: Preprocess Intervals and Step 2: Collect Read Counts, plus 10 more sections
  • Runs Shell scripts from its folder

What it does

Bio Copy Number Gatk Cnv is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines.

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/run_gatk_cnv.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

  • Following GATK best practices
  • Integrating CNV calling with other GATK variant pipelines

Example prompts

  • “/bio-copy-number-gatk-cnv”

Requirements

  • A Bash shell

Workflow steps

7 steps, taken from the step headings in SKILL.md.

  1. Preprocess Intervals
  2. Collect Read Counts
  3. Create Panel of Normals
  4. Denoise Read Counts
  5. Collect Allelic Counts
  6. Model Segments
  7. Call Copy Ratio Segments

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 Copy Number Gatk Cnv loads about 2.1k tokens when it runs. Until then it costs about 68 tokens; SKILL.md has 379 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~68
When it runs · the whole SKILL.md, loaded when a task matches
~2.1k

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 379 words (~2,057 tokens).

“Reference examples tested with: GATK 4.5+”

— opening of SKILL.md by FreedomIntelligence
name
bio-copy-number-gatk-cnv
tool_type
cli
primary_tool
gatk

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-copy-number-gatk-cnv of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/run_gatk_cnv.sh
  • usage-guide.md

Open the folder on GitHubat commit b1f9b6e

Compare with similar skills

Bio Copy Number Gatk Cnv 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.

Bio Copy Number Gatk Cnv compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Copy Number Gatk Cnv this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k—~2.1kAutomated safety check: PassNone
Bio Copy Number Gatk CnvGPTomics/bioSkills1.2k2 repos~3.9kAutomated safety check: PassMIT
Bio Copy Number Subclonal Copy NumberGPTomics/bioSkills1.2k2 repos~3.5kAutomated safety check: PassMIT
Bio Copy Number Cnv AnnotationGPTomics/bioSkills1.2k2 repos~3.4kAutomated safety check: PassMIT
Bio Copy Number Cnv VisualizationGPTomics/bioSkills1.2k2 repos~3.3kAutomated safety check: PassMIT
Bio Copy Number Allele Specific Copy NumberGPTomics/bioSkills1.2k2 repos~4kAutomated safety check: PassMIT

Similar skills

  • Bio Copy Number Gatk Cnv

    GPTomics/bioSkills

    Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments)…

    1.2k GitHub starsUsed in 2 repos~3.9k tokens
    DatabasesAuto-check passed

  • Bio Copy Number Subclonal Copy Number

    GPTomics/bioSkills

    Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2.

    1.2k GitHub starsUsed in 2 repos~3.5k tokens
    Research & ScienceAuto-check passed

  • Bio Copy Number Cnv Annotation

    GPTomics/bioSkills

    Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content.

    1.2k GitHub starsUsed in 2 repos~3.4k tokens
    Research & ScienceAuto-check passed

  • Bio Copy Number Cnv Visualization

    GPTomics/bioSkills

    Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers.

    1.2k GitHub starsUsed in 2 repos~3.3k tokens
    Data & AnalyticsAuto-check passed

  • Bio Copy Number Allele Specific Copy Number

    GPTomics/bioSkills

    Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and…

    1.2k GitHub starsUsed in 2 repos~4k tokens
    Business, Finance & HRAuto-check passed

  • Bio Copy Number Germline Cnv Interpretation

    GPTomics/bioSkills

    Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV and AnnotSV for semi-automated…

    1.2k GitHub starsUsed in 2 repos~3k tokens
    EducationAuto-check passed

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Questions about Bio Copy Number Gatk Cnv

What does Bio Copy Number Gatk Cnv do?

Call copy number variants using GATK best practices workflow. Bio Copy Number Gatk Cnv is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Call copy number variants using GATK best practices workflow.

When should I use Bio Copy Number Gatk Cnv?

Bio Copy Number Gatk Cnv fits situations like: following GATK best practices; integrating CNV calling with other GATK variant pipelines.

How do I install Bio Copy Number Gatk Cnv in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-gatk-cnv -a claude-code`. Or copy the skill folder (skills/bio-copy-number-gatk-cnv in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-copy-number-gatk-cnv in your project. Claude Code loads it when a task matches its description.

How do I install Bio Copy Number Gatk Cnv in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-gatk-cnv -a codex`. Or copy the skill folder (skills/bio-copy-number-gatk-cnv in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-copy-number-gatk-cnv in your project. Codex loads it when a task matches its description.

Can I use Bio Copy Number Gatk Cnv 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-copy-number-gatk-cnv -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-copy-number-gatk-cnv, .gemini/skills/bio-copy-number-gatk-cnv, .github/skills/bio-copy-number-gatk-cnv and .opencode/skills/bio-copy-number-gatk-cnv in your project.

What does Bio Copy Number Gatk Cnv need to run?

Going by SKILL.md and its folder, Bio Copy Number Gatk Cnv needs a shell for the scripts in its folder. Our summary lists: A Bash shell.

Does Bio Copy Number Gatk Cnv 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 Copy Number Gatk Cnv 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 Copy Number Gatk Cnv use?

No licence was found for Bio Copy Number Gatk Cnv or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Copy Number Gatk Cnv use?

About 2.1k tokens (SKILL.md is roughly 8.2k 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 Copy Number Gatk Cnv?

Skills that share tags, products or a category with Bio Copy Number Gatk Cnv: Bio Copy Number Gatk Cnv (GPTomics/bioSkills, 1.2k stars), Bio Copy Number Subclonal Copy Number (GPTomics/bioSkills, 1.2k stars), Bio Copy Number Cnv Annotation (GPTomics/bioSkills, 1.2k stars) and Bio Copy Number Cnv Visualization (GPTomics/bioSkills, 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 Copy Number Gatk Cnv?

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.