plink2-gwas-analysis

npx skills add BioTender-max/awesome-bio-agent-skills --skill plink2-gwas-analysis --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# PLINK2 — GWAS and Population Genetics ## Overview PLINK2 is the high-performance successor to PLINK 1.9, designed for genome-wide association studies (GWAS) and population genetics analysis on large cohorts. It processes genotype data in PLINK binary format (.bed/.bim/.fam), VCF, and BGEN formats — performing sample and variant quality control (QC), kinship estimation, principal component analysis (PCA), and linear/logistic regression association testing. PLINK2 is 10–100× faster than PLINK 1.9 on most tasks due to multithreading and optimized I/O. Output files are compatible with downstream visualization (Manhattan/QQ plots) and meta-analysis tools. ## When to Use - Running GWAS on a case-control or quantitative trait cohort after genotyping array QC - Performing sample QC: missingness, heterozygosity outliers, sex check, cryptic relatedness - Computing genome-wide LD pruning for PCA or relatedness estimation - Running PCA on genotype data to identify population stratification - Converting between PLINK binary, VCF, and BGEN formats - Filtering variants by MAF, HWE, missingness, or INFO score in VCF/imputed data - Use **regenie** or **SAIGE** instead for biobank-scale GWAS (>100

Skip install if already present
if command -v plink2 >/dev/null 2>&1; then
echo "plink2 already installed: $(plink2 --version)"
else
wget https://s3.amazonaws.com/plink2-assets/alpha6/plink2_linux_avx2_20241112.zip
unzip plink2_linux_avx2_20241112.zip
chmod +x plink2
export PATH="$PWD:$PATH"
plink2 --version
fi