CGIL Centre for Genetic Improvement of Livestock
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  Version 1.10

QTL and Marker Simulator

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. 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 establish mutation-drift equilibrium and create linkage disequilibrium.

  • 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 and also sequence data 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 in cM.

  • 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 with pre-defined MAF threshold and QTL can be selected.

  • 16-bit version allows for assigning unique alleles to each founder.

  • Complete linkage disequilibrium in the first historical generation can be generated.

  • Calculates LD decay 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 (can be calculated and inputted by the user) 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 unnecessary data.

  • Equipped with fast and high-quality pseudo-random number generators.

  • Allows flexible input parameter file.

  • Computationally efficient.

  • Download   (Last update: July 12, 2013)

  • Windows version

  • Linux version

  • Mac version

  • 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