Figure 1.

Workflow of cophesim has three stages: (1) Input stage, where the input data (can be provided in one of the three formats: Plink, MS and GENOME, see the user manual - Supplementary File 1) along with the other input parameters (such as causal variants with size effects, output format, etc.) is prepared for phenotype simulation; (2) Phenotype simulation stage, where different types of phenotypic traits are simulated: dichotomous, continuous and time-to-event (‘survival’); (3) Output stage – the final stage, where simulated phenotype data are packed to various formats in order to be directly usable by six GWAS tools: EMMAX, BLOSSOC, Plink, QTDT, TASSEL and GenABEL. Summary statistics are generated at the output stage as well.