Population Structure

Analyze genetic ancestry and population stratification using PCA and ADMIXTURE.

Principal Component Analysis (PCA)

PLINK 2.0 PCA

# Basic PCA (10 PCs)
plink2 --bfile data --pca 10 --out pca_results

# More PCs
plink2 --bfile data --pca 20 --out pca_results

# Approximate PCA (faster for large datasets)
plink2 --bfile data --pca 10 approx --out pca_results