g Documentation

Status	Applies to	Owner
Pre-release draft	main branch as of 2026-07-01 public docs	Public user docs

g is a pre-release GWAS engine focused on BGEN-backed REGENIE Step 2 association scans. It exposes a REGENIE-style CLI and TOML configuration while using Rust for native file handling and JAX for quantitative and binary association kernels.

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

Choose Your Path

I want to...	Read
understand what `g` can run	Getting Started
install on a workstation or cluster	Installation
run a first Step 2 scan	Quickstart
port an existing REGENIE Step 2 workflow	Compatibility, then CLI
understand required input files	Input Files
find and interpret output files	Output Files, then Algorithm
resume or inspect an interrupted run	Resume and Manifest
run on GPU or SLURM	GPU and Clusters
tune or measure performance	Performance Guide
fix an error	Troubleshooting

Reference Pages

Topic	Canonical page
CLI grammar, flags, boolean semantics, and exit behavior	CLI
TOML sections, merge order, effective config, and defaults policy	Configuration
Genotype, sample, phenotype, covariate, and prediction files	Input Files
Run directories, Parquet dataset schema, and telemetry files	Output Files
Strict resume behavior, manifest compatibility, and graceful interruption	Resume and Manifest
Statistical models and result interpretation	Algorithm
GPU, cluster, and SLURM operation	GPU and Clusters
Performance tuning and measurement	Performance Guide
Common failures and first checks	Troubleshooting

Development-team documentation starts at Development. Internal scratchpad notes are kept under documentation/scratchpad/ and may be stale.