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

• convert
• cluster
• validate
• annotate
• pairing
• summary

All steps in the MAVIS pipeline are called following the main mavis entry point. The usage menu can be viewedby 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 thewiki.If you have a question or issue that is not answered there (or already a github issue) please submita github issue to ourgithub page or contact us by email atmavis@bcgsc.ca

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

pip install -U setuptools pip wheelpip 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 installinstructions in theuser 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.