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bioRxiv · 10.1101/2025.08.15.670378

Fast Phenotype Simulation for Genotype Representation Graphs

Syam, A.·Adonizio, C.·Wei, X.
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Abstract

MotivationThe Genotype Representation Graph (GRG) [DeHaas et al., 2025] is a graph representation of whole genome polymorphisms, designed to encode the variant hard-call information in phased whole genomes. It encodes the geno-types 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. ResultsGrgPhenoSim contains all the primary functionalities of a phenotype simulator, uses a standardized output, and supports customized simulations. Grg-PhenoSim is dozens to hundreds of times faster than tstrait [Tagami et al., 2024], a fast ancestral recombination graph-based phenotype simulator, when the sample size ranges from thousands to hundreds of thousands samples. AvailabilityThe GrgPhenoSim library and use-case demonstrations are available at https://github.com/aprilweilab/grg_pheno_sim The documentation for GrgPhenoSim is hosted at https://grgl.readthedocs.io/en/latest/index.html

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Syam, A., Adonizio, C., Wei, X.. 2025-08-20. Fast Phenotype Simulation for Genotype Representation Graphs. https://doi.org/10.1101/2025.08.15.670378

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