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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
phenosim--A software to simulate phenotypes for testing in genome-wide association studies.
Torsten Günther1, Inka Gawenda, Karl J Schmid
1Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany. torsten.guenther@uni-hohenheim.de
BMC Bioinformatics
|July 1, 2011
Summary
Phenosim is a new software tool that adds phenotypes to simulated genotypes, aiding genetic architecture studies. This tool helps assess factors influencing the power of genome-wide association studies (GWAS) in diverse population genetics scenarios.
Area of Science:
- Population Genetics
- Genomics
- Computational Biology
Background:
- Understanding the genetic basis of complex traits in natural populations is crucial.
- Genome-wide association studies (GWAS) are essential for linking genetic variation to phenotypic variation.
- Coalescent simulations are widely used to model genetic variation under various population parameters.
Purpose of the Study:
- To introduce phenosim, a novel software for generating phenotypes in simulated genotypes.
- To enable the simulation of both qualitative and quantitative phenotypes, including additive and epistatic effects.
- To facilitate the assessment of factors impacting GWAS power in population genetics.
Main Methods:
- Phenosim integrates phenotypes with genotypes from time-efficient coalescent simulations.
- The software allows for the partitioning of phenotypic variation into additive and epistatic components.
- Output formats are compatible with standard GWAS software.
Main Results:
- Phenosim successfully generates phenotypic data for simulated genotypes.
- The software can model complex genetic architectures, including epistasis.
- Demonstrated applicability through a simulated GWAS in Arabidopsis thaliana.
Conclusions:
- Combined use of coalescent simulations and phenosim generates valuable datasets for power analysis.
- These datasets aid in evaluating the influence of demography, genetic architecture, and selection on GWAS.
- Phenosim is freely accessible, promoting its use in population genetic research.
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