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 is a drop-in replacement for the pairwise linkage disequilibrium (LD) modes of vcftools 0.1.17, --hap-r2 and --geno-r2, which population-genetic pi