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bio-workflows-gwas-pipeline

Official

End-to-end GWAS workflow from VCF to results.

Data & Analytics#gwas#pca#genotype#phenotype#qc#plink
Authorstellaromics
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Genome-wide association studies can be complex and error-prone; this workflow provides an end-to-end pipeline from raw genotype data to association results, including QC, population structure adjustment, and association testing for case-control or quantitative traits.

Core Features & Use Cases

  • End-to-end GWAS: QC, LD pruning, PCA, and regression-based association tests.
  • Flexible trait support: Works for both binary (case-control) and quantitative traits with covariate handling.
  • Outputs: Manhattan and QQ plots, significant hits, and summary statistics for downstream interpretation.

Quick Start

Run an end-to-end GWAS from VCF to association results using PLINK2, including QC, LD pruning, PCA, and association testing.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: bio-workflows-gwas-pipeline
Download link: https://github.com/stellaromics/fast-bioinfo/archive/main.zip#bio-workflows-gwas-pipeline

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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