vibe

Variant Interpretation using Biological Evidence

Requirements

For building/testing:

For generating a local TDB dataset needed by the application:

For running the application:

Java 8
Human Phenotype Ontology (HPO)
A local TDB dataset (see above).

Preparations

Before using the tool, be sure all steps below are done (certain steps can be skipped if already present/configured):

Creating an executable jar

Download and install Apache Maven
Run mvn clean install from the git repository directory.

Preperations for unit-testing.

Download and configure the environment so that the Jena scripts can be used.
Run TestNGPreprocessing.sh (optionally with extra arguments required for certain tests).

Creating a local TDB dataset.

Download and configure the environment so that the Jena scripts can be used.
Download the required files (DisGeNET, SIO).
Run tdbloader2 --loc /path/to/store/TDB /path/to/disgenet/dump/*.ttl /path/to/sio-release.owl

Running the application

Usage

java -jar vibe-with-dependencies.jar [-h] [-v] -t <FILE> [-w <FILE> -n <NAME> -m <NUMBER>] -o <FILE> [-s <NAME>] [-l] -p <HPO ID> [-p <HPO ID>]...

Examples

Using only the user-defined phenotypes with the output being sorted based on the highest gene-disease association score present per gene:

java -jar vibe-with-dependencies.jar -v -t TDB/ -s gda_max -o results.tsv -p HP:0002996 -p HP:0001377

Using the user-defined phenotypes and phenotypes that are related to them with a maximum distance of 1 with the output sorted based on the Disease Specificity Index:

java -jar vibe-with-dependencies.jar -v -t TDB/ -w hp.owl -n distance -m 1 -s dsi -o results.tsv -p HP:0002996

Using the user-defined phenotypes and their (grand)children with a maximum distance of 2 with the output sorted based on the Disease Pleiotropy Index:

java -jar vibe-with-dependencies.jar -v -t TDB/ -w hp.owl -n children -m 2 -s dpi -o results.tsv -p HP:0002996

freerkvandijk/vibe