DISCRIMINATOR

DISCRIMINATOR is a command-line tool that assigns provisional pathogenicity classifications to CNVs based upon genomic location overlap with user-supplied presumed benign and pathogenic intervals.

Requirements

DISCRIMNATOR requires Python (2.7.X) in a Linux operating system to run. Python3 is currently not supported. A list of the required Python modules is listed below. If you want to run the pre-processing script, bedtools is also required.

Required Python Modules:

• progress
• networkx; version 1.8.1
• intervaltree

Input

For processing, DISCRIMINATOR requires patient CNV datasets to be in tab-delimited with three columns with the header: 'Sample', 'Chromosome Region', 'Event'.

1. The first column contains the patient or sample identifier.
2. The second column contains the genomic coordinates for a single CNV in the following format (chr:start-end).
3. The third column contains the direction of the CNV (accepted values: CN Gain or CN Loss)

To modify additional parameters for assigning provisional pathogenicity classifications, see the User Manual.

Command to run DISCRIMINATOR:

python CODE/INTERFACE_DISCRIMINATOR.py

Citation

If you use the software, please cite: TBD

Future Improvements

• Support for Python3
• Integration of bedtools pre-processing script with the rest of DISCRIMINATOR.