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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

There are 3 major steps to setting up and installingMAVIS. If you are a developer contributing to mavis, please see theinstructions for developers page instead

In addition to the python package dependencies,MAVIS also requires an aligner to be installed.Currently the only aligners supported areblat andbwa mem.For MAVIS to run successfully the aligner must be installed and accessible on the path.If you have a non-standard install you may find it useful to edit the PATH environment variable. For example

export PATH=/path/to/directory/containing/blat/binary:$PATH

blat is the default aligner. To configure MAVIS to usebwa mem as a default instead, use theMAVIS environment variables. Make sure to specify BOTH of the variables below to change the default aligner.

export MAVIS_ALIGNER='bwa mem'export MAVIS_ALIGNER_REFERENCE=/path/to/mem/fasta/ref/file

After this has been installed MAVIS itself can be installed throughpip

The easiest way to installMAVIS is through the python package manager, pip. If you do not have python3 installed it can be foundhere

Ensuring you have a recent version of pip and setuptools will improve the install experience. Older versions of pip and setuptools may have issues with obtaining some of the mavis python dependencies

pip install --upgrade pip"setuptools<58"

or (for Anaconda users)

conda update pip"setuptools<58"

If this is not a clean/new python install it may be useful to set up mavis in avirtual python environment

Then install mavis itself

pip install mavis

This will install mavis and its python dependencies.

Alternatively you can use thebootstrap/buildout to install mavis into bin/mavis

git clone https://github.com/bcgsc/mavis.gitcd mavispip install zc.buildoutpython bootstrap.pybin/buildout

This will install mavis and its python dependencies into eggs inside the cloned mavis directory which can be used by simply running bin/mavis

AfterMAVIS is installed thereference files must be generated (or downloaded) before it can be run. A simple bash script to download the hg19 reference files and generate a MAVIS environment file is provided under mavis/tools for convenience.

cd /path/to/where/you/want/to/put/the/fileswget https://raw.githubusercontent.com/bcgsc/mavis/master/tools/get_hg19_reference_files.shbash get_hg19_reference_files.shsource reference_inputs/hg19_env.sh

Once the above 3 steps are completeMAVIS is ready to be run.See the MAVIStutorial to learn about running MAVIS.

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.