Agent skill

Gwas Pipeline

End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing.

MITAuto-check passedResearch & Science

Install Gwas Pipeline

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-pipeline -a claude-code

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

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-pipeline --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/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/gwas-pipeline .claude/skills/gwas-pipeline && 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/

Paste into Claude Code

Install the "gwas-pipeline" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-pipeline into .claude/skills/gwas-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-pipeline", 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

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-pipeline

Type 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.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-pipeline -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-pipeline --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/gwas-pipeline .agents/skills/gwas-pipeline && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "gwas-pipeline" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-pipeline into .agents/skills/gwas-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-pipeline", 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.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-pipeline -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-pipeline --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/gwas-pipeline .cursor/skills/gwas-pipeline && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "gwas-pipeline" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-pipeline into .cursor/skills/gwas-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-pipeline", 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

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/gwas-pipeline

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-pipeline -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-pipeline --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/gwas-pipeline .gemini/skills/gwas-pipeline && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "gwas-pipeline" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-pipeline into .gemini/skills/gwas-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-pipeline", 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.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-pipeline

Installs 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).

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-pipeline -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/gwas-pipeline .github/skills/gwas-pipeline && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "gwas-pipeline" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-pipeline into .github/skills/gwas-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-pipeline", 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.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-pipeline -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-pipeline --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/gwas-pipeline .opencode/skills/gwas-pipeline && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "gwas-pipeline" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-pipeline into .opencode/skills/gwas-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-pipeline", 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: gwas-pipeline
GitHub stars: 1.2k
Used in: 1 other repo
Token cost: ~1.4k tokens
SKILL.md length: 499 words
Files: 11
Skills in repo: 104
Repo updated: Oct 9, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing.

Works in 6 steps: Genotype QC via PLINK2: Sample/variant… → REGENIE Step 1: Whole-genome ridge… → REGENIE Step 2: Single-variant… → …
Tasks that involve Bioinformatics
SKILL.md covers Why This Exists, Core Capabilities, Input Formats and Workflow, plus 6 more sections
Runs Python scripts from its folder; calls python and conda

What it does

Gwas Pipeline is an agent skill from ClawBio/ClawBio. End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing. Produces Manhattan plots, QQ plots, clumped lead variants, and structured summary statistics.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files (for example `gwas_pipeline.py`, `tests/__init__.py` and `tests/test_gwas_pipeline.py`).

It sits in Research & Science, covering Bioinformatics and Data analysis. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

Tasks that involve Bioinformatics
Tasks that involve Data analysis

Example prompts

“/gwas-pipeline”

Requirements

Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

Genotype QC via PLINK2: Sample/variant missingness, MAF, HWE, LD pruning
REGENIE Step 1: Whole-genome ridge regression with LOCO predictions
REGENIE Step 2: Single-variant association (Firth logistic / linear)
Visualisation: Manhattan plot, QQ plot with lambda GC
Post-GWAS: Lead variant extraction at genome-wide significance (P < 5e-8)
Reproducibility: Full command logging, parameter tracking, software versions

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. 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 (Python), which the agent can run.
Shell commands in SKILL.md call:
- python
- conda
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- pubmed.ncbi.nlm.nih.gov
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

Gwas Pipeline loads about 1.4k tokens when it runs. Until then it costs about 59 tokens; SKILL.md has 499 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~59
When it runs · the whole SKILL.md, loaded when a task matches: ~1.4k

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 ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 499 words, ~1,416 tokens.

Download SKILL.mdSave it as .claude/skills/gwas-pipeline/SKILL.md (or your agent's skills folder). This skill also uses 10 other files; get the full folder from GitHub.

name: gwas-pipeline
description: End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing. Produces Manhattan plots, QQ plots, clumped lead variants, and structured summary statistics.
license: MIT
metadata.version: 0.1.0
metadata.author: Reza
metadata.tags: gwas, association-testing, regenie, plink2, population-genetics, biobank, quality-control

📊 GWAS Pipeline

You are GWAS Pipeline, a specialised ClawBio agent for genome-wide association studies. Your role is to automate best-practice QC and association testing from genotype files to publication-ready results.

Why This Exists

Without it: Researchers must orchestrate PLINK2 and REGENIE manually, writing hundreds of lines of bash, managing dozens of parameters, and applying field-standard QC thresholds by hand
With it: A single command runs the full QC cascade, REGENIE two-step regression, and post-GWAS visualisation on any genotype dataset
Why ClawBio: Grounded in Anderson et al. (2010) QC thresholds and Mbatchou et al. (2021) REGENIE methodology — not ad hoc parameter choices. Every command logged for reproducibility

Core Capabilities

Genotype QC via PLINK2: Sample/variant missingness, MAF, HWE, LD pruning
REGENIE Step 1: Whole-genome ridge regression with LOCO predictions
REGENIE Step 2: Single-variant association (Firth logistic / linear)
Visualisation: Manhattan plot, QQ plot with lambda GC
Post-GWAS: Lead variant extraction at genome-wide significance (P < 5e-8)
Reproducibility: Full command logging, parameter tracking, software versions

Input Formats

Format	Extension	Required Fields	Example
PLINK binary	`.bed` + `.bim` + `.fam`	Standard PLINK format	`example.bed`
BGEN	`.bgen`	BGEN v1.2+ with sample info	`example.bgen`
Phenotype	`.txt`	FID, IID, trait column(s)	`phenotype_bin.txt`
Covariate	`.txt`	FID, IID, covariate columns	`covariates.txt`

Workflow

Validate: Check input files exist, detect format, verify binaries on PATH
QC (PLINK2): Variant missingness, sample missingness, MAF, HWE filtering; LD pruning for Step 1
Step 1 (REGENIE): Whole-genome ridge regression on LD-pruned genotyped variants with LOCO
Step 2 (REGENIE): Single-variant association with Firth correction (binary) or linear regression (quantitative)
Post-GWAS: Parse results, compute lambda GC, extract lead variants, generate plots
Report: Write report.md, result.json, summary statistics TSV, and reproducibility bundle

CLI Reference

bash

# Demo mode (REGENIE example data, binary trait Y1)
python skills/gwas-pipeline/gwas_pipeline.py --demo --output /tmp/gwas_demo

# Real data
python skills/gwas-pipeline/gwas_pipeline.py \
  --bed /path/to/data --pheno pheno.txt --covar covar.txt \
  --trait-type bt --trait Y1 --output results/

# Via ClawBio runner
python clawbio.py run gwas-pipe --demo

Show full SKILL.md (215 more words)Show less

Demo

bash

python clawbio.py run gwas-pipe --demo

Expected output: A full GWAS report on REGENIE's official 500-sample, 1000-variant example dataset with binary trait Y1, including QC summary, REGENIE Step 1/2 output, Manhattan plot, QQ plot with lambda GC, and reproducibility bundle.

Dependencies

Required (external binaries):

plink2 >= 2.0 — genotype QC and LD operations
regenie >= 3.0 — two-step whole-genome regression

Install via conda: CONDA_SUBDIR=osx-64 conda create -n clawbio-gwas -c conda-forge -c bioconda plink2 regenie

Python (standard library + matplotlib):

matplotlib >= 3.7 — Manhattan and QQ plots
numpy >= 1.24 — QQ plot expected quantiles

Safety

Local-first: All computation runs locally via PLINK2/REGENIE subprocesses
Disclaimer: Every report includes the ClawBio medical disclaimer
Audit trail: Every PLINK2/REGENIE command logged to reproducibility/commands.sh
No hallucinated science: All QC thresholds trace to Anderson et al. 2010 / REGENIE documentation

Integration with Bio Orchestrator

Trigger conditions — the orchestrator routes here when:

User mentions GWAS, association testing, Manhattan plot, or case-control study
User provides genotype files (BED/BIM/FAM, BGEN, VCF) with a phenotype file

Chaining partners:

gwas-lookup: Downstream — look up lead variants across federated databases
gwas-prs: Downstream — compute polygenic risk scores from summary statistics
variant-annotation: Downstream — annotate lead variants with VEP/ClinVar

Citations

Mbatchou et al. (2021) — REGENIE: computationally efficient whole-genome regression. Nature Genetics 53:1097–1103
Chang et al. (2015) — Second-generation PLINK. GigaScience 4:7
Anderson et al. (2010) — Data quality control in genetic case-control association studies. Nature Protocols 5:1564–1573

Files

SKILL.md and 10 other files in skills/gwas-pipeline of ClawBio/ClawBio.

SKILL.md
example_data/covariates.txt
example_data/example.bed
example_data/example.bgen
example_data/example.bim
example_data/example.fam
example_data/phenotype_bin.txt
example_data/test_bin_out_firth_Y1.regenie
gwas_pipeline.py
tests/__init__.py
tests/test_gwas_pipeline.py

Open the folder on GitHubat commit dece754

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 ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

BioTender-max/awesome-bio-agent-skillsskills/clawbio/gwas-pipeline

Compare with similar skills

Gwas Pipeline 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.

Gwas Pipeline compared with similar skills
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Tooluniverse Polygenic Risk Scorewu-yc/LabClaw	1.1k	2 repos	~3.7k	Automated safety check: Pass	None	6 mo ago
Lncrna Regulatory Network Construction Analysisaipoch/medical-research-skills	1.9k	—	~2.7k	Automated safety check: Pass	MIT	23 days ago
Bio Population Genetics Linkage DisequilibriumGPTomics/bioSkills	1.2k	1 repos	~4.7k	Automated safety check: Pass	MIT	1 mo ago

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Questions about Gwas Pipeline

What does Gwas Pipeline do?

End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing. Gwas Pipeline is an agent skill from ClawBio/ClawBio. End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing.

When should I use Gwas Pipeline?

Gwas Pipeline fits situations like: tasks that involve Bioinformatics; tasks that involve Data analysis.

How do I install Gwas Pipeline in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill gwas-pipeline -a claude-code`. Or copy the skill folder (skills/gwas-pipeline in ClawBio/ClawBio) into .claude/skills/gwas-pipeline in your project. Claude Code loads it when a task matches its description.

How do I install Gwas Pipeline in Codex?

Run `npx skills add ClawBio/ClawBio --skill gwas-pipeline -a codex`. Or copy the skill folder (skills/gwas-pipeline in ClawBio/ClawBio) into .agents/skills/gwas-pipeline in your project. Codex loads it when a task matches its description.

Can I use Gwas Pipeline 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 ClawBio/ClawBio --skill gwas-pipeline -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gwas-pipeline, .gemini/skills/gwas-pipeline, .github/skills/gwas-pipeline and .opencode/skills/gwas-pipeline in your project.

What does Gwas Pipeline need to run?

Going by SKILL.md and its folder, Gwas Pipeline needs Python for the scripts in its folder and the command-line tools its instructions call (python and conda). Our summary lists: Python 3.

Does Gwas Pipeline access the network?

SKILL.md names 1 domain. As links in the text: pubmed.ncbi.nlm.nih.gov. This is read from the text; nothing was executed.

Is Gwas Pipeline 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 Gwas Pipeline use?

Gwas Pipeline is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Gwas Pipeline use?

About 1.4k tokens (SKILL.md is roughly 5.7k 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 Gwas Pipeline?

Skills that share tags, products or a category with Gwas Pipeline: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 33k stars), Single-Cell Initial Analysis (LigphiDonk/Oh-my--paper, 739 stars), Tooluniverse Polygenic Risk Score (wu-yc/LabClaw, 1.1k stars) and Lncrna Regulatory Network Construction Analysis (aipoch/medical-research-skills, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Gwas Pipeline?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,155 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 9, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Gwas Pipeline

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

📊 GWAS Pipeline

Why This Exists

Core Capabilities

Input Formats

Workflow

CLI Reference

Demo

Dependencies

Safety

Integration with Bio Orchestrator

Citations

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Gwas Pipeline