HAPGEN2: simulation of multiple disease SNPs

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Second-generation PLINK: rising to the challenge of larger and richer datasets (2014, methodology): “For each marker, calculate and save the seven possible increments in a lookup table, and then refer to the table when updating partial sums.”
Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies (2014, methodology): “Starting from the 1000 Genomes (1 KG) European samples, we used HAPGEN [40] to simulate fine-mapping data sets over 10 Kb loci.”
Polygenic scores via penalized regression on summary statistics (2016, methodology): “We then used Hapgen2 (Su et al., 2011) to generate genotypes, using the CEU (Utah residents with Northern and Western European ancestry) population of the 1000 Genome data as a base.”