MAVIS is python command-line tool for the post-processing of structural variant calls.
The general MAVIS pipeline consists of six main stages
There are 3 major steps to setting up and installing MAVIS
Install non-python dependencies
Before MAVIS can be installed, the non-python dependencies will need to be installed.
After these have been installed MAVIS itself can be installed through pip
These include: an aligner (blat or bwa mem) and samtools.
The easiest way to install MAVIS is through the python package manager, pip
pip install mavis
This will install mavis and its python dependencies.
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 email@example.com
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.