LIRICAL Advanced Options

Most users will not need these commands, which are hidden from the normal user menu. The LIRICAL code base contains functionalities that we used to develop and validate the program, and we describe them here briefly.

Generating the background files

LIRICAL uses the files src/main/resources/background/background-hg19.tsv and src/main/resources/background/background-hg38.tsv to estimate the expected population frequencies of predicted pathogenic variants. The important classes as BackgroundFrequencyCommand.java and GenicIntoleranceCalculator.java. You do not need to generate the files yourself to run Exomiser (they are included in the resource files). The following command generates the files.

java -jar target/LIRICAL.jar background -e /path/to/exomiser/1811_hg19 -g hg19