Genetic and population analysis GWAsimulator: A rapid whole genome simulation program

Summary: GWAsimulator implements a rapid moving-window algo-rithm to simulate genotype data for case-control or population sam-ples from genomic SNP chips. For case-control data, the program generates cases and controls according to a user-specified multi-locus disease model, and can simulate specific regions if desired. The program uses phased genotype data as input and has the flexi-bility of simulating genotypes for different populations and different genomic SNP chips. When the HapMap phased data are used, the simulated data have similar local LD patterns as the HapMap data. As genome-wide association (GWA) studies become increasingly popular and new GWA data analysis methods are being developed, we anticipate that GWAsimulator will be an important tool for evalu-ating performance of new GWA analysis methods. Availability: The C++ source code, executables for Linux, Win-dows, and MacOS, manual, example data sets and analysis pro