Oligopipe documentation#

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oligopipe is a Python package for the discovery of candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction developed at the Interuniversity Institute of Bioinformatics in Brussels.

It is available as a CLI that takes arguments (see --help) either directly or via a YAML configuration file.

What can you do with oligopipe?#

The CLI tool currently contains three modules:

Commands:
  Run oligopipe {command} -h to get detailed help

  {predict,prioritize,config}
    predict             Run a VarCoPP prediction
    prioritize          Run a prioritization analysis with Hop
    config              Show the template config file

The PREDICT and PRIORITIZE modules both take in your variant data, preprocess it according to your submitted settings, and either predict with VarCoPP or prioritize with HOP the candidate pathogenic variant combinations in any gene pair.

With CONFIG you can show a template for the input config YAML which can be used instead of / in combination with the command-line arguments. The latter will always get priority if both are given for a specific argument.

Important note#

The results of these pipelines are based on predictive tools. They are provided for research, educational and informational purposes only and the pathogenicity predictions should be subject to further scientific and clinical investigation.
It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.