SUMMIT

Summary-statistics-based Unified Method for Multivariate Inference of Traits

SUMMIT estimates heritability and genetic correlation from GWAS summary statistics, computes LD scores from reference genotypes, and fits gene–environment interaction models and polygenic scores.

Main features

• Genome-wide and windowed LD-score estimation.
• SNP heritability and genetic correlation, including annotation partitions.
• Batch analysis of many traits and annotation models.
• Gene–environment interaction (G×E) and environment-dependent residual variance.
• Joint models of multiple continuous or categorical environments.
• G×E polygenic score fitting, scoring, and calibration.

Genotype input can be PLINK BED hard calls or biallelic diploid PGEN dosages. See the user guide for the inputs and availability of each method.

Install

You need Conda, Python 3.10 or newer, and a C++17 compiler with OpenMP support. The environment file supplies the Python and numerical-library dependencies. Linux is recommended; the direct generalized G×E backend requires Linux.

git clone https://github.com/bronsonj98/SUMMIT.git
cd SUMMIT
conda env create -f environment.yml
conda activate summit
python -m pip install .
summit --help
summit-pgs --help

See Installation for compiler setup, development installs, and the additional build needed for generalized G×E reference estimation.

Try it

Generate a small synthetic dataset and estimate partitioned LD scores:

python example/prepare_example_inputs.py
bash example/estimate_partitioned_gwldscore.sh
bash example/h2_ldscore.sh

Examples write to example/out/. They illustrate the commands; their small sample sizes are unsuitable for evaluating statistical performance.

Documentation

• Input files
• LD scores
• Heritability and genetic correlation
• Batch analyses
• G×E models
• Multiple environments
• G×E polygenic scores
• Real-data results
• Benchmarks

Citation

Jeong, M., Pazokitoroudi, A., Liu, Z., & Sankararaman, S. (2024). Scalable summary statistics-based heritability estimation method with individual genotype level accuracy. Genome Research, gr.279207.124. Paper.