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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 Help

All steps in the MAVIS pipeline are called following the main mavis entry point. The usage menu can be viewed by running without any arguments, or by giving the -h/--help option

mavis -h

Help sub-menus can be found by giving the pipeline step followed by no arguments or the -h options

mavis cluster -h

Common problems and questions are addressed on the wiki. If you have a question or issue that is not answered there (or already a github issue) please submit a github issue to our github page or contact us by email at

Getting Started

The simplest way to use MAVIS is via Singularity. The MAVIS docker container used by singularity will take care of installing the aligner as well.

pip install -U setuptools pip wheel
pip install mavis_config  # also installs snakemake

Now you will run mavis via Snakemake as follows

snakemake \
    -j <MAX JOBS> \
    --configfile <YOUR CONFIG> \
    --use-singularity \
    -s Snakefile

For other installation options which do not use docker/singularity see the comprehensive install instructions in the user manual


If you use MAVIS as a part of your project please cite

Reisle,C. et al. (2018) MAVIS: Merging, Annotation, Validation, and Illustration of Structural variants. Bioinformatics.