g - GPU-oriented REGENIE Step 2 GWAS engine

g is a pre-release GWAS engine for BGEN-backed REGENIE Step 2 association scans. It exposes a REGENIE-style CLI and TOML configuration, uses Rust for native file handling, and uses JAX for quantitative and binary association kernels. Python embedding is not a supported API.

g does not implement REGENIE Step 1. Use upstream regenie to produce Step 1 prediction lists, then use g for Step 2 scans.

Current Scope

Area	Status
Quantitative REGENIE Step 2 (--qt)	Primary supported workflow
Binary score-test Step 2 (--bt)	Supported, evolving
Binary approximate Firth fallback (--bt --binary-fallback firth_approximate)	Implemented, parity and performance sensitive
REGENIE Step 1	Not implemented
BGEN 1.2 input	Supported
BED/PGEN input	Unsupported; absent from the CLI and rejected as unknown
Output	Chunked Parquet datasets only
GPU execution	Supported through JAX when the environment is configured

Install

g is installed from a Git checkout because it is not published on PyPI.

git clone https://github.com/kirilledition/g.git
cd g
uv python install 3.14
uv sync --python 3.14 --no-dev
uv run g --help

For GPU installs, cluster installs, and development setup, use Installation.

Minimal Run Shape

uv run g regenie \
  --qt \
  --bgen /path/to/genotypes.bgen \
  --sample /path/to/genotypes.sample \
  --phenoFile /path/to/phenotypes.tsv \
  --phenoCol phenotype_name \
  --covarFile /path/to/covariates.tsv \
  --covarCol age --covarCol sex \
  --pred /path/to/regenie_step1_pred.list \
  --out /path/to/output/g_regenie2

See Quickstart for quantitative, binary, approximate-Firth, multi-phenotype, GPU, and Parquet-output examples.

Documentation Map

User-facing behavior lives under documentation/public/:

• Public guide index
• Compatibility and current scope
• CLI reference
• Configuration reference
• Input files
• Output files
• Resume and manifests
• Performance guide
• Troubleshooting

Implementation and contributor guidance lives under documentation/development/:

• Development index
• Architecture
• Configuration frontend
• Testing and parity
• Benchmarking
• Style guide

Internal scratchpad notes live under documentation/scratchpad/. They are not part of the primary published navigation and may be stale.

Documentation Build

just docs-serve
just docs-build

The published documentation site is expected at:

https://kirilledition.github.io/g/

Code Size

Generated from Git-tracked files under crates/ and src/ using cloc.

Language	Files	Blank	Comment	Code
Rust	120	5,622	971	53,056
Python	106	3,126	2,308	23,302
TOML	9	30	8	217
Total	235	8,778	3,287	76,575

cloc version: 2.09.