European LD proxies lose tagging for 43% of GWAS leads in the African panel: a chromosome 22 analysis with SwiftLD, an 826-fold faster, byte-identical vcftools LD

SwiftLD computes vcftools LD outputs byte-identically while running 826-fold faster on chromosome 22 regions of 1000 Genomes, enabling rapid r2/D/D' calculations.

• Why it matters: LD proxy selection is computationally heavy in population-genetic pipelines, and slow LD computation can bottleneck GWAS follow-up across multiple panels.
• What they did: SwiftLD is a drop-in replacement for vcftools 0.1.17 --hap-r2 and --geno-r2, validated on three chromosome 22 regions (503–2,504 samples) with correctness-gated coding and 167,749 differential tests.
• The result: Using chromosome 22, European LD proxies retain r2 ≥ 0.8 for 57.4% of GWAS leads in the African panel, versus 85.6%–92.7% in other panels (98.1% in a European split-half control).

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