GSUB

GSUB (Gwas-by-SUBtraction) is a command line tool to perform GWAS-by-subtraction. It uses closed-form solutions to estimate the associations between each SNP and the two latent components for two traits (i.e., $\gamma_1$ and $\gamma_2$ in the diagram below). Its inputs are two GWAS summary statistics for two traits, and the outputs are two summary statistics for the two latent factors. The $\gamma_2$ is shown in red is because it is the parameter of interest: the SNP effect on the latent factor for trait 2 after regressing out the factor for trait 1.

Manual

Please see the wiki for the detailed manual of GSUB.

Version History

• September 19, 2023: Initial release.

Citation

If you use GSUB, please cite:
Wu et al. (2024). Pervasive biases in proxy genome-wide association studies based on parental history of Alzheimer’s disease. Nature Genetics, https://doi.org/10.1038/s41588-024-01963-9.

Contact

For questions and comments, please open a Github issue (preferred) or contact Yuchang Wu at [email protected] or Stephen Dorn at [email protected].