Abstract Motivation The Genotype Representation Graph (GRG) is a graph representation of whole genome polymorphisms, designed to encode the variant hard-call information in phased whole genomes. It encodes the genotypes as an extremely compact graph that can be traversed efficiently, enabling dynamic programming-style algorithms on applications such as genome-wide association studies that run faster on biobank-scale data than existing alternatives. To facilitate scalable statistical genetics, we present GrgPhenoSim, an extremely fast phenotype simulator for GRGs, suitable for simulating phenotypes on biobank-scale datasets. Results GrgPhenoSim contains all the primary functionalities of a phenotype simulator, uses a standardized output, and supports customized simulations. GrgPhenoSim is dozens to hundreds of times faster than tstrait, a fast ancestral recombination graph-based phenotype simulator, when the sample size ranges from thousands to hundreds of thousands samples. Availability The GrgPhenoSim library and use-case demonstrations are available at https: //github. com/aprilweilab/grgₚhenoₛim The documentation for GrgPhenoSim is hosted at https: //grgl. readthedocs. io/en/stable/examplesₐndₐpplications. html#phenotype-simulation
Syam et al. (Mon,) studied this question.