Abstract
BackgroundPopulation-wide genotypic and phenotypic data is frequently used to predict the disease risk or genetic/phenotypic values, or to localize genetic variations responsible for complex traits. GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with desired genetic parameters and underlying genetic architectures.ResultsThe model implemented in GPOPSIM is presented, and the code has been made freely available to the community. Data simulated by GPOPSIM is a good mimic to the real data in terms of genome structure and trait underlying genetic architecture.ConclusionsGPOPSIM would be a useful tool for the methodological and theoretical studies in the population and quantitative genetics and breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0173-4) contains supplementary material, which is available to authorized users.
Highlights
Population-wide genotypic and phenotypic data is frequently used to predict the disease risk or genetic/phenotypic values, or to localize genetic variations responsible for complex traits
We present Genome-wide population simulation (GPOPSIM): a simulation tool for population genetic data based on Mutation-drift equilibrium (MDE)
Besides the features predefined by users, e.g. marker density, minor allele frequency (MAF) and linkage disequilibrium (LD) can typically reflect the characteristic of the simulated genotypic data
Summary
Population-wide genotypic and phenotypic data is frequently used to predict the disease risk or genetic/phenotypic values, or to localize genetic variations responsible for complex traits. We present GPOPSIM: a simulation tool for population genetic data based on MDE. Genetic and phenotypic values Based on the genome structure generated in the historical population, the trait and QTL parameters, GPOPSIM simulates genetic and phenotypic values for each individual in the current population.
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