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Overview

In addition to the python package interface, users may also opt to use viprs via commandline scripts. The commandline interface is designed to be user-friendly and to provide a variety of options for the user to customize the inference process.

When you install viprs using pip, the commandline scripts are automatically installed on your system and are available for use. The following scripts are meant to facilitate the entire pipeline of polygenic score inference, from fitting and estimating the posterior distribution of the variant effect sizes to predicting the PRS for a set of test individuals and evaluating the performance of the PRS predictions on held out samples.

  • viprs_fit: This script is used to fit the variational PRS model to the GWAS summary statistics and to estimate the posterior distribution of the variant effect sizes. The script provides a variety of options for the user to customize the inference process, including the choice of prior distributions and the choice of optimization algorithms.

  • viprs_score: This script is used to predict the PRS for a set of individuals using the estimated variant effect sizes from the viprs_fit script. This is the script that generates the PRS per individual.

  • viprs_evaluate: This script is used to evaluate the performance of the PRS predictions using the PRS computed in the previous step. The script provides a variety of options for the user to customize the evaluation process, including the choice of performance metrics and the choice of evaluation datasets.

TODO

  • Create a nextflow pipeline that runs all of the above steps in a single command.