The general[MAVIS](http://mavis.bcgsc.ca) pipeline consists of six main stages

- convert

-[cluster](http://mavis.bcgsc.ca/docs/latest/mavis.cluster.html#mavis-cluster)

-[validate](http://mavis.bcgsc.ca/docs/latest/mavis.validate.html#mavis-validate)

-[annotate](http://mavis.bcgsc.ca/docs/latest/mavis.annotate.html#mavis-annotate)

-[pairing](http://mavis.bcgsc.ca/docs/latest/mavis.pairing.html#mavis-pairing)

-[summary](http://mavis.bcgsc.ca/docs/latest/mavis.summary.html#mavis-summary)

-[cluster](https://mavis.readthedocs.io/en/latest/package/mavis/cluster)

-[validate](https://mavis.readthedocs.io/en/latest/package/mavis/validate)

-[annotate](https://mavis.readthedocs.io/en/latest/package/mavis/annotate)

-[pairing](https://mavis.readthedocs.io/en/latest/package/mavis/pairing)

-[summary](https://mavis.readthedocs.io/en/latest/package/mavis/summary)

There are 3 major steps to setting up and installing[MAVIS](http://mavis.bcgsc.ca). If you are a developer contributing to mavis, please see the[instructions for developers page](http://mavis.bcgsc.ca/docs/latest/development.html) instead

There are 3 major steps to setting up and installing[MAVIS](http://mavis.bcgsc.ca). If you are a developer contributing to mavis, please see the[instructions for developers page](https://mavis.readthedocs.io/en/latest/development) instead

In addition to the python package dependencies,[MAVIS](http://mavis.bcgsc.ca) also requires an aligner to be installed.

Currently the only aligners supported are[blat](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-blat) and[bwa mem](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-bwa).

Currently the only aligners supported are[blat](https://mavis.readthedocs.io/en/latest/glossary/#blat) and[bwa mem](https://mavis.readthedocs.io/en/latest/glossary/#bwa).

For MAVIS to run successfully the aligner must be installed and accessible on the path.

If you have a non-standard install you may find it useful to edit the PATH environment variable. For example

[blat](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-blat) is the default aligner. To configure MAVIS to use[bwa mem](http://mavis.bcgsc.ca/docs/latest/glossary.html#term-bwa) as a default instead, use the

[MAVIS environment variables](http://mavis.bcgsc.ca/configuration.html#environment-variables). Make sure to specify BOTH of the variables below to change the default aligner.

[MAVIS environment variables](https://mavis.readthedocs.io/en/latest/configuration/settings/). Make sure to specify BOTH of the variables below to change the default aligner.

export MAVIS_ALIGNER='bwa mem'

After[MAVIS](http://mavis.bcgsc.ca) is installed the[reference files](http://mavis.bcgsc.ca/docs/latest/mavis_input.html#reference-input-files) must be generated (or downloaded) before it can be run. A simple bash script to download the hg19 reference files and generate a MAVIS environment file is provided under mavis/tools for convenience.

After[MAVIS](http://mavis.bcgsc.ca) is installed the[reference files](https://mavis.readthedocs.io/en/latest/inputs/reference) must be generated (or downloaded) before it can be run. A simple bash script to download the hg19 reference files and generate a MAVIS environment file is provided under mavis/tools for convenience.

cd /path/to/where/you/want/to/put/the/files

Once the above 3 steps are complete[MAVIS](http://mavis.bcgsc.ca) is ready to be run.

See the MAVIS[tutorial](http://mavis.bcgsc.ca/docs/latest/pipeline.html#mavis-mini-tutorial) to learn about running MAVIS.

See the MAVIS[tutorial](https://mavis.readthedocs.io/en/latest/tutorials/mini) to learn about running MAVIS.

There are many ways that single reads or paired-end reads can act as

support for an SV call.

In the figure above the red rectangle represents a deletion structural

variant. The arrows are types of single or paired-end reads supporting

orientation but that the fragment size should be abnormal (for large

deletions).

Flanking read pair evidence for a deletion event. the read pairs will

have a larger than expected fragment size when mapped to the reference

Flanking read pair evidence for an insertion event. The read pairs

will have a smaller than expected fragment size when mapped to the

Flanking read pair evidence for a tandem duplication event. The read

pairs will have an abnormal orientation but still the same strands as

Flanking read pair evidence for an inversion. Both breakpoints have

left orientation.

Flanking read pair evidence for an inversion. Both breakpoints have

right orientation.

Flanking read pair evidence for a translocation. (B1) the first

breakpoint with a left orientation. (B2) the second breakpoint with a

right

orientation.

Flanking read pair evidence for a translocation. (B1) the first

breakpoint with a right orientation. (B2) the second breakpoint with a

Flanking read pair evidence for an inverted translocation. Both

breakpoints have left

orientation.

Flanking read pair evidence for an inverted translocation. Both

breakpoints have right

region) and similarly flanking pairs which support an insertion may be

compatible flanking evidence for a duplication

The event depicted above may be called as either a duplication or an

insertion (depending on the input call). If the even were called as a

Basic Terms used in describing read pairs are shown above: fragment

size: the distance between the pair; read length: the length of the

This gives us an idea of when to judge an fragment size as abnormal and

where we expect our normal read pairs fragment sizes to fall.

Distribution of fragment sizes (absolute values) of proper read pairs.

The black curve representings the fit for a normal distribution using

limit of how large the range can be. This is further refined taking into

account the range spanned by the[flanking read pair](../../glossary/#flanking-read-pair) evidence and the position of the opposing breakpoint.



Calculation of the left-oriented breakpoint by flanking reads. Reads

mapped to the breakpoint are shown in grey. The read on the right (black



After a breakpoint has been called we can narrow the interval of

expected fragment sizes using the size of the event. (Left) The colored

breakpoints. Only valid combinations have been shown. see



Classification Decision Tree. The above diagram details the decsion

logic for classifying events based on the orientation, strand and

encompassed between the breakpoints (for example in a deletion event the

genes that would be deleted).



Gene level annotations at each breakpoint. Note: genes which fall

between a breakpoint pair, encompassed genes, will not be present for

be. MAVIS will calculate all possibilities according to the following

model.



The default splicing pattern is a list of pairs of donor and acceptor

splice sites

strand of the transcript) donor splice sites are paired with all

following as seen below



Multiple abrogated acceptors sites. As one can see above this

situation will result in 3 different splicing patterns depending on

which donor is paired with the 2nd acceptor

site



Multiple abrogated donor sites. As one can see above this situation

will result in 3 different splicing patterns depending on which acceptor

(`mavis.constants.SPLICE_TYPE.COMPLEX`{.interpreted-text

role="attr"})



the breakpoint.



(A-D) The breakpoint lands in an exon and the five prime portion of

the transcript is retained. (A) The original splicing pattern showing

Resource Requirements (MAVIS 1.8.0) for each validation job of the

COLO829 tumour genome. The BAM file for the tumour genome is 127GB.

constant which is expected since, unlike validation, anntotation does

not read more data in for more events.

Resource Requirements (MAVIS 1.8.0) for each annotation job of the

COLO829 tumour genome. The events which passed validation (see above)

compute cluster. will generate submission scripts and a wrapper bash

script for the user to execute on their cluster head node.

The MAVIS pipeline is highly configurable. Some pipeline steps

(cluster, validate) are optional and can be automatically skipped. The

This will submit a series of jobs with dependencies.

Dependency graph of MAVIS jobs for the standard pipeline setup. The

notation on the arrows indicates the SLURM setting on the job to add the