phenosim

phenosim simulates phenotypes for genotypes produced by coalescent simulations to model additive and epistatic genetic effects, generate qualitative and quantitative traits, and assess statistical power in genome-wide association studies.

Key Features:

• Integration with Coalescent Simulations: Reads outputs from coalescent simulators and uses those genotypes to simulate qualitative and quantitative phenotypes according to user-defined parameters and demographic models.
• Phenotypic Variation Modeling: Partitions phenotypic variation into additive effects and epistatic interactions among causal genetic variants.
• Output Compatibility: Produces output formats compatible with GWAS tools for downstream association analyses.
• Assessment of Statistical Power: Simulates phenotypes alongside genotypes to evaluate how demography, genetic architecture, and selection influence the statistical power of association methods.

Scientific Applications:

• Genome-wide association study simulation: Generates genotype–phenotype datasets for GWAS, including use cases in Arabidopsis thaliana.
• Power and method evaluation: Assesses the impact of demography, genetic architecture, and selection on detection of causal variants and statistical power of association methods.
• Complex trait and population genetics research: Models additive and epistatic interactions and multiple trait types to investigate genetic architectures and trait evolution.

Methodology:

Consumes genotype data produced by coalescent simulations and adds phenotypes (qualitative and quantitative) according to specified parameters, partitioning effects into additive components and epistatic interactions.