JointSV analyses multiple BND sample files in VCF format produced by Gridss in order to detect Structural Variations by the Joint-call method.

Clone or download the GitHub repository.

JointSV requires Python 3.7 (newer versions may also work).

Some Python libraries are also required. They can be downloaded using the pip tool from the directory that contains the JointSV source code.

$ pip install -r requirements.txt

Place each input sample in a separate VCF file. JointSV does not support multi-sample inputs.

Run the program like this:

$ python3 jointsv.py input/*.vcf -o output.vcf

Alternatively, instead of enumerating the input files or using wildcards, a directory can be used instead. In that case, all files (of any extension) in that directory will be used as input. Subdirectories will not be traversed. This is useful to overcome the limitations around the maximum number of files in the CLI. Example:

$ python3 jointsv.py input/ -o output.vcf

• FILE1, FILE2...: name of the input files. If any of them is actually a directory, then all files in that directory will be used as input. The files will be processed in alphabetical filename order, regardless of the order in which they appear in the command line.

• -o/--output FILE: name of the output file. If omitted, the default is output.vcf. If set to -, then the output is written to stdout.

• --chromosome chr3,chr7: indicates which chromosomes are to be processed, as comma-separated values. If this parameter is omitted, all chromosomes are included.

We've integrated some tests in order to verify that when we change things in the code we are not breaking the functionality of it with these changes. In order to run the tests, run the following command line:

 pytest tests.py

If your python does not include pytest, you can install it running the following command on your terminal:

pip3 install pytest

Dr. Emma Rath - Victor Chang Cardiac Research Institute

The following Atlassian employees have participated in writing this software through a collaboration project between the Atlassian Foundation and the Victor Chang Cardiac Research Institute:

• Luis Lainez
• Peter Grasevski
• Diego Berrueta