Linkage Disequilibrium

Calculate LD statistics, prune correlated variants, and identify haplotype blocks.

PLINK LD Calculations

Pairwise r²

# All pairs within window
plink2 --bfile data --r2 --ld-window-kb 1000 --ld-window-r2 0.2 --out ld_results

# With SNP names in output
plink2 --bfile data --r2 inter-chr --ld-window-r2 0 --out all_pairs

# Squared correlation matrix
plink2 --bfile data --r2-phased square --out ld_matrix