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.
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Use gwas-pipeline to run local QC and REGENIE association testing on [genotype files] with [phenotype file] and [covariate file], producing summary statistics, lead variants, Manhattan and QQ plots, a reproducibility bundle, and the required medical disclaimer.
Required inputs
[genotype files]
[phenotype file]
[covariate file]
User-approved starter prompt based on a pinned source version; check current skill requirements before running. Task evidence ↗
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
Report: Write report.md, result.json, summary statistics TSV, and reproducibility bundle
CLI Reference
# 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
Demo
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.