Fregene: Simulation of realistic sequence-level data in populations and ascertained samples

Background: FREGENE simulates sequence-level data over large genomic regions in large populations. Because, unlike coalescent simulators, it works forwards through time, it allows complex scenarios of selection, demography, and recombination to be modelled simultaneously. Detailed tracking of sites under selection is implemented in FREGENE and provides the opportunity to test theoretical predictions and gain new insights into mechanisms of selection. We describe here main functionalities of both FREGENE and SAMPLE, a companion program that can replicate association study datasets. Results: We report detailed analyses of six large simulated datasets that we have made publicly available. Three demographic scenarios are modelled: one panmictic, one substructured with migration, and one complex scenario that mimics the principle features of genetic variation in major worldwide human populations. For each scenario there is one neutral simulation, and one with a complex pattern of selection...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Marc Chadeau-Hyam, Clive J. Hoggart, Paul F. O'Reilly, John C. Whittaker, Maria De Iorio, David J. Balding
• Keywords: BMCBI 2008, Large Genomic Regions, Scenarios, Selection