Overview
Linkage disequilibrium (LD) and linkage analyses have been used extensively to identify
quantitative trait loci (QTL) in human and livestock. Owing to the recent developments
in genotyping technologies, dense marker maps are now available for several livestock
species. Even though genotyping costs have substantially declined, large scale
genome-wide association studies are still costly. For this reason many studies in
livestock suffer from small sample size or from low density of markers. However,
simulation is a highly valuable tool for assessing and validating new proposed methods
for association studies at very low cost. During the last few decades, simulation has
played a major role in answering a wide variety of questions in genomics. Several
software have been developed for simulating genomes especially in human research. However most
of the developed software tools do not provide functionality required for many of the applications in
livestock.
QMSim was developed to simulate large scale genomic data in livestock populations.
QMSim is a family based simulator, which can also take into account predefined
evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is
basically carried out in two steps: In the first step, a historical population is simulated
to establish mutation-drift equilibrium and, in the second step, recent population structures are
generated, which can be complex. QMSim allows for a wide range of parameters to be
incorporated in the simulation models in order to produce appropriate simulated data.
Features
Simulates historical generations to created linkage disequilibrium.
Establishes mutation-drift equilibrium.
Recombination is appropriately modeled. Interference is allowed.
Multiple chromosomes, each with different or similar density of markers and QTL maps, can be generated.
Very dense marker map can be simulated.
Missing genotypes and genotyping errors can be simulated.
Markers can be either SNP or microsatellites.
Males and females can have different genome length.
Unbalanced sex ratio is also allowed in historical populations.
Additive QTL effects can be simulated with different distributions, such as gamma, normal or uniform.
In addition to QTL effects, polygenic effect can be included.
After mutation-drift equilibrium, polymorphic marker panel and QTL can be selected. This greatly reduces the computational requirements for the recent population(s).
16-bit version allows for assigning unique alleles to each founder.
Complete linkage disequilibrium in the first historical generation can be generated.
Calculates LD in specified generations.
Population expansion or bottleneck is allowed for both historical and recent populations.
Selection and culling of breeding population can be carried out based on different criteria, such as phenotypes, estimated breeding values and true breeding values.
More than one litter size with predefined probabilities can be considered.
Multiple recent populations or lines can be simulated. Crossing between populations or lines is allowed.
Multiple populations can be analyzed jointly for estimating breeding values and computing inbreeding.
Creates detailed output files. Outputs can be customized to avoid saving unwanted data.
Equipped with fast and high-quality pseudo-random number generators.
Allows flexible input parameter file.
Computationally efficient in terms of both time and memory.
Download
(Last update: February 09, 2009)
Windows
Linux - Opteron precessor
Linux - Xeon precessor
QMSim documentation (PDF)
Citing QMSim
Sargolzaei, M. and F. S. Schenkel. 2009. QMSim: a large-scale genome simulator for livestock.
Bioinformatics, 25: 680-681. First published January 28, 2009, doi:10.1093 /bioinformatics/btp045
Contact
Centre for Genetic Improvement of Livestock
