About

MAVIS is a pipeline to merge and validate input from different structural variant callers into a single report. The pipeline consists five of main steps

• cluster
• validate
• annotate
• pairing
• summary

Getting started

There are 3 major steps to setting up and installing MAVIS

1. 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

2. Install MAVIS

pip install mavis

This will install mavis and its python dependencies.

3. Build reference files

After MAVIS is installed the reference files must be generated before it can be run.

Once the above 3 steps are complete MAVIS is ready to be run. See running the pipeline.

Non-python dependencies

Aligner

In addition to the python package dependencies, MAVIS also requires an aligner to be installed. Currently the only aligners supported are blat and bwa mem. For MAVIS to run successfully the aligner must be installed and accessible on the path. If you have a non-std 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 use bwa mem as a default instead, use the MAVIS environment variables. Both the aligner and aligner reference settings should be specified

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

Samtools

Samtools is only used in sorting and indexing the intermediary output bams. Eventually this will hopefully be accomplished through pysam only.