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Non-python Dependencies

MAVIS integrates with SV callers, job schedulers, and aligners. While some of these dependencies are optional, all currently supported options are detailed below. The versions column in the tables below list all the versions which were tested for each tool. Each version listed is known to be compatible with MAVIS.

Job Schedulers

MAVIS v3 uses snakemake to handle job scheduling


Two aligners are supported bwa and blat (default). These are both included in the docker image by default.

Name Version(s) Environment Setting
blat 36x2 36 MAVIS_ALIGNER=blat
bwa mem 0.7.15-r1140 0.7.12 MAVIS_ALIGNER='bwa mem'


When setting the aligner you will also need to set the aligner_reference to match