Command Line Interface¶

Gelex provides a comprehensive command-line interface for genomic analysis. The tool follows a subcommand-based structure similar to git or plink2.

Available Subcommands¶

The following subcommands cover the complete genomic analysis workflow:

Subcommand	Description
fit	Fit Bayesian models (BayesAlphabet) and estimate marker effects.
assoc	Perform GWAS using mixed linear models (GBLUP) with LOCO.
grm	Compute Genomic Relationship Matrices (Yang, Zeng, Vitezica).
predict	Predict phenotypes for new samples using trained effects.
simulate	Simulate phenotypes based on real genotypes and genetic architectures.

Global Options¶

Option	Description
`-h, --help`	Show help message and exit.
`-v, --version`	Print version information and exit.

Basic Usage Pattern¶

To get help for a specific subcommand, use:

gelex <subcommand> --help