Overview

In addition to the python package interface, users may also opt to use some of magenpy's functionalities via commandline scripts. The commandline interface is limited at this point to mainly simulating complex traits and computing LD matrices.

When you install magenpy using pip, the commandline scripts are automatically installed on your system and are available for use. The available scripts are:

• magenpy_ld: This script is used to compute LD matrices from genotype data in plink BED format. The script provides a variety of options for the user to customize the LD computation process, including the choice of LD estimator, storage and compression options, etc.

• magenpy_simulate: This script is used to simulate complex traits with a variety of genetic architectures. The script provides a variety of options for the user to customize the simulation process, including the choice of genetic architecture, the proportion of causal variants, the effect sizes, etc.