PIGEON (PolygenIc Gene-Environment interactiON) is a Python3-based command line tool for estimating polygenic gene-environment (GxE) interactions using GWIS (and GWAS) summary statistics.

The PIGEON software can be used to

1. estimate the GxE variance components (proportion of phenotypic variance explained by genome-wide GxE interactions).
2. perform hypothesis-free scans for PGSxE across many PGS (without the need to calculate PGS).

PIGEON can be downloaded via git clone https://github.com/qlu-lab/PIGEON

Please see the wiki for the short tutorials describing the two basic functions (estimating GxE variance components and hypothesis-free scans for PGSxE), as well as the detailed manual of PIGEON.

Please see the FAQ for the commonly asked question regrading PIGEON.

• Dec 12, 2022: Initial release.

If you use PIGEON, please cite

Miao, J., Song, G., Wu, Y., Hu, J., Wu, Y., Basu, S., Andrews, J. S., Schaumberg, K., Fletcher, J. M., Schmitz, L. L., & Lu, Q. (2022). PIGEON: a statistical framework for estimating gene–environment interaction for polygenic traits. Nat Hum Behav (2025). https://doi.org/10.1038/s41562-025-02202-9

For questions and comments, please open a GitHub issue (preferred) or contact Jiacheng Miao at [email protected].

• QUAIL (QUAntile Integral Linear model) is a quantile regression-based framework to estimate genetic effects on the variance of quantitative traits.

Part of the code is adapted from LDSC. We thank Dr. Bulik-Sullivan for sharing their code.