About¶
MAVIS is a pipeline to merge and validate input from different structural variant callers into a single report. The pipeline consists four of main steps
Getting started¶
Install¶
Installing Dependencies¶
to install dependencies, use the requirements.txt file
pip install -r requirements.txt
Running Unit Tests¶
to run the tests
nosetests --with-coverage --cover-html --cover-html-dir=coverage --cover-package=mavis --cover-erase
Building the documentation¶
can build the documentation directly using make
cd docs
make html
this will generate html documentation that can be viewed in a browser by opening the index.html file
Input Files¶
The requirements are described in JIRA and are listed below. These pertain to the input files from the various tools you want to merge. The expected input columns are given below. All columns must be given except: individual breakpoint strand columns do not need to be given if the input is not stranded and opposing_strands has been specified
Required Columns¶
Conversion scripts¶
The output of the calls to be merged from the various tools must first be put into a standard/common format. For the tools we commonly use the locations to conversion scripts are listed below
Reference Files¶
There are several reference files that are required for full functionality of the MAVIS pipeline. If the same
reference file will be reused often then the user may find it helpful to set reasonable defaults. Default values
for any of the reference file arguments can be configured through MAVIS_ prefixed environment variables.
| file | file type/format | environment variable |
|---|---|---|
| reference genome | fasta | MAVIS_REFERENCE_GENOME |
| annotations | JSON or text/tabbed | MAVIS_ANNOTATIONS |
| masking | text/tabbed | MAVIS_MASKING |
| template metadata | text/tabbed | MAVIS_TEMPLATE_METADATA |
If the environment variables above are set they will be used as the default values when any step of the pipeline script is called (including generating the template config file)
Reference Genome¶
These are the sequence files in fasta format that are used in aligning and generating the fusion sequences.
Examples:
Annotations¶
This is a custom file format. Essentially just a tabbed or JSON file which contains the gene, transcript, exon, translation and protein domain positional information
Warning
the load_reference_genes() will
only load valid translations. If the cds sequence in the annotation is not
a multiple of CODON_SIZE or if a
reference genome (sequences) is given and the cds start and end are not
M and * amino acids as expected the translation is not loaded
Example of the JSON file structure can be seen below
[
{
"name": string,
"start": int,
"end": int
"aliases": [string, string, ...],
"transcripts": [
{
"name": string,
"start": int,
"end": int,
"exons": [
{"start": int, "end": int, "name": string},
...
],
"cdna_coding_start": int,
"cdna_coding_end": int,
"domains": [
{
"name": string,
"regions": [
{"start" aa_start, "end": aa_end}
],
"desc": string
},
...
]
},
...
]
},
...
}
This reference file can be generated from any database with the necessary information. There is a basic perl script to generate the JSON file using a connection to the Ensembl perl api.
Template Metadata¶
This is the file which contains the band information for the chromosomes. This is only used during visualization.
Examples:
chr1 0 2300000 p36.33 gneg
chr1 2300000 5400000 p36.32 gpos25
chr1 5400000 7200000 p36.31 gneg
chr1 7200000 9200000 p36.23 gpos25
chr1 9200000 12700000 p36.22 gneg
Masking File¶
File which contains regions that we should ignore calls in. This can be used to filter out regions with known false positives, bad mapping, centromeres, telomeres etc. An example is shown below
#chr start end name
chr1 0 2300000 centromere
chr1 9200000 12700000 telomere
Running the Pipeline¶
The pipeline can be run calling the main script (see below) followed the pipeline step. The usage menu can be viewed by running the without any arguments, or by giving the -h/–help option
Example:
python bin/mavis_run.py
Help sub-menus can be found by giving the pipeline step followed by no arguments or the -h options
python bin/mavis_run.py cluster -h
Determining Input Parameters¶
There are some parameters that need to be computed from the bam files. This can generally be done by running the profile_bam.py script found in the tools directory
>>> python tools/profile_bam.py /path/to/bam/file -c 16
profiling chr 16
FINAL
average 396.72
average stdev 98.89
median 383
median distrib[0.80] stdev 59.56
median distrib[0.90] stdev 72.80
median distrib[0.95] stdev 82.20
median distrib[0.99] stdev 93.94
median distrib[1.00] stdev 99.84
Generally giving it a single chromosome will be enough reads but it can be given as many chromosomes/templates as required. This script calculates the median insert size and then the standard deviation (wrt to the median not mean) from all or a portion of the distribution of insert sizes
Generating a config file¶
The pipeline can be run in steps or it can be configured using a configuration file and setup in a single step. Scripts will be generated to run all steps following clustering. The configuration file can be built from scratch or a template can be output as shown below
>>> mavis_run.py pipeline template.cfg --write
This will create a template config file called template.cfg which can then be edited by the user.