phenosim

BACKGROUND: There is a great interest in understanding the genetic architecture
of complex traits in natural populations. Genome-wide association studies (GWAS)
are becoming routine in human, animal and plant genetics to understand the
connection between naturally occurring genotypic and phenotypic variation.
Coalescent simulations are commonly used in population genetics to simulate
genotypes under different parameters and demographic models. RESULTS: Here, we
present phenosim, a software to add a phenotype to genotypes generated in
time-efficient coalescent simulations. Both qualitative and quantitative
phenotypes can be generated and it is possible to partition phenotypic variation
between additive effects and epistatic interactions between causal variants. The
output formats of phenosim are directly usable as input for different GWAS tools.
The applicability of phenosim is shown by simulating a genome-wide association
study in Arabidopsis thaliana. CONCLUSIONS: By using the coalescent approach to
generate genotypes and phenosim to add phenotypes, the data sets can be used to
assess the influence of various factors such as demography, genetic architecture
or selection on the statistical power of association methods to detect causal
genetic variants under a wide variety of population genetic scenarios. phenosim
is freely available from the authors' website http://evoplant.uni-hohenheim.de.

phenosim--A software to simulate phenotypes for testing in genome-wide association studies.

phenosim is a software tool for genome-wide association studies (<a href="https://www.genome.gov/genetics-glossary/Genome-Wide-Association-Studies" target="_blank" rel="noopener">GWAS</a>) to simulate/add qualitative and quantitative phenotypes to genotypes generated by coalescent simulations. See also <a href="https://bioinformaticshome.com/tools/gwas/gwas.html#gsc.tab=0" target="_blank" >Free Genome-wide Association Study (GWAS) Tools</a>.

phenosim

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