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 supports simulating complex traits, computing LD matrices, and extracting, pruning, or expanding variant sets from pre-computed 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:

• mgp_compute_ld: 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.

• mgp_simulate: 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.

• mgp_extract_ld: Extract dense LD submatrices for SNP lists or genomic regions.

• mgp_prune_ld: Prune variants by LD threshold using pre-computed LD matrices.

• mgp_expand_ld: Expand focal SNPs to include LD neighbors from pre-computed LD matrices.

If you use uv, you can also run the scripts without permanently installing magenpy into the active environment:

uvx --from magenpy mgp_compute_ld -h
uvx --from magenpy mgp_simulate -h