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Contents

  • G2P
  • SIMER
  • GCTA
  • HAPGEN
  • simGWAS
  • sim1000G

G2P

  • SHORT NAME:G2P
  • FULL NAME:A Genome-Wide-Association-Study Simulation Tool for Genotype Simulation, Phenotype Simulation, and Power Evaluation
  • YEAR:2019
  • DESCRIPTION:a Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation
  • CITATION:Tang, You, and Xiaolei Liu. "G2P: a genome-wide-association-study simulation tool for genotype simulation, phenotype simulation and power evaluation." Bioinformatics 35.19 (2019): 3852-3854.
  • URL: https://github.com/XiaoleiLiuBio/G2P

SIMER

  • SHORT NAME:SIMER
  • FULL NAME:Data Simulation for Life Science and Breeding
  • DESCRIPTION: Data Simulation for Life Science and Breeding
  • CITATION: coming soon
  • URL: https://github.com/xiaolei-lab/SIMER#genotype-data

GCTA

  • SHORT NAME: GCTA
  • FULL NAME:Genome-wide complex trait analysis (GCTA)
  • YEAR:2010
  • DESCRIPTION:GCTA-GREML analysis:GCTA can simulate a GWAS based on real genotype data.
  • URL: https://yanglab.westlake.edu.cn/software/gcta/#GWASSimulation

simGWAS

  • SHORT NAME:simGWAS
  • FULL NAME:simGWAS
  • YEAR:2019
  • DESCRIPTION: a fast method for simulation of large scale case–control GWAS summary statistics
  • URL: https://github.com/chr1swallace/simGWAS
  • CITATION:Fortune, Mary D., and Chris Wallace. "simGWAS: a fast method for simulation of large scale case–control GWAS summary statistics." Bioinformatics 35.11 (2019): 1901-1906.

HAPGEN2

  • SHORT NAME:HAPGEN2
  • FULL NAME:HAPGEN2
  • YEAR:2011
  • DESCRIPTION:HAPGEN2 is a an updated version of the program HAPGEN, which simulates case control datasets at SNP markers. The new version can now simulate multiple disease SNPs on a single chromosome, on the assumption that each disease SNP acts independently and are in Hardy-Weinberg equilibrium. We also supply a R package that can simulate interaction between the disease SNPs.
  • CITATION:Su, Zhan, Jonathan Marchini, and Peter Donnelly. "HAPGEN2: simulation of multiple disease SNPs." Bioinformatics 27.16 (2011): 2304-2305.
  • URL: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html

sim1000G

  • SHORT NAME:sim1000G
  • FULL NAME:sim1000G
  • YEAR:2019
  • DESCRIPTION:a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs
  • CITATION:Dimitromanolakis, Apostolos, et al. "sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs." BMC bioinformatics 20.1 (2019): 1-9.
  • URL: https://github.com/adimitromanolakis/sim1000G

twas_sim

  • SHORT NAME:twas_sim
  • FULL NAME:twas_sim
  • YEAR:2023
  • DESCRIPTION: A python software leveraging real genotype data to simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on the complex trait.
  • URL: https://github.com/mancusolab/twas_sim
  • CITATION:Wang, X., Lu, Z., Bhattacharya, A., Pasaniuc, B., & Mancuso, N. (2023). twas_sim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis. Bioinformatics, btad288.