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A Structural Variant Post-Processing Package

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MAVIS is python command-line tool for the post-processing of structural variant calls. The general MAVIS pipeline consists of six main stages

Getting started

There are 3 major steps to setting up and installing MAVIS

  1. Install Aligner

Before MAVIS can be installed, the non-python dependency will need to be installed. After these have been installed MAVIS itself can be installed through pip

The user may configure MAVIS to run using blat or bwa mem.

  1. Install MAVIS

The easiest way to install MAVIS is through the python package manager, pip

pip install mavis

This will install mavis and its python dependencies.

  1. Build reference files

After MAVIS is installed the reference files must be generated (or downloaded) before it can be run.

Once the above 3 steps are complete MAVIS is ready to be run. See running the pipeline.


If you have a question or issue that is not answered in the FAQs please submit an issue to our github page or contact us by email at

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