XSim: Simulation of Descendants from Ancestors with Sequence Data

Abstract

Real or imputed high-density SNP genotypes are routinely used for genomic prediction and genome-wide association studies. Many researchers are moving toward the use of actual or imputed next-generation sequence data in whole-genome analyses. Simulation studies are useful to mimic complex scenarios and test different analytical methods. We have developed the software tool XSim to efficiently simulate sequence data in descendants in arbitrary pedigrees. In this software, a strategy to drop-down origins and positions of chromosomal segments rather than every allele state is implemented to simulate sequence data and to accommodate complicated pedigree structures across multiple generations. Both C++ and Julia versions of XSim have been developed.

Keywords: GenPred; genome-wide association studies; genomic prediction; genomic selection; pedigree; sequence data; shared data resource; simulation.

Figure 1

An example to illustrate the simulation strategy (crossover sites indicated by ↕).