A Structural Variant Post-Processing Package
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
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 email@example.com
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 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
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