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.
- 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.
- 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.