domains / families / science / linkage-disequilibrium

linkage-disequilibrium

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Computes linkage disequilibrium (r2, D', composite Rogers-Huff r2), prunes correlated variants, clumps GWAS summary statistics to lead SNPs, and defines haplotype blocks with PLINK 1.9/2.0 and scikit-allel. r2 and D' answer different questions - r2 (= chi2/N) is the tagging and GWAS-power currency, D' marks observed recombination and is upward-biased for rare variants. PLINK 2.0 has no bare --r2 (split into --r2-phased and --r2-unphased); pruning (--indep-pairwise, genotype-blind) and clumping (--clump, p-value-aware) are distinct operations that are constantly confused. The clumping or fine-mapping LD reference must be ancestry-matched or it fails silently into false credible sets. Use when calculating LD, pruning variants for PCA or structure, clumping GWAS hits, or selecting tag SNPs. For QC see plink-basics; for PCA see population-structure; fine-mapping is causal-genomics/fine-mapping.

When to use

• calculating LD
• pruning variants for PCA or structure
• clumping GWAS hits
• selecting tag SNPs
• defining haplotype blocks
• LD decay analysis

When not to use

• QC
• PCA
• fine-mapping
• causal-genomics
• phased haplotypes
• phasing-imputation
• haplotype-phasing
• association-testing

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