Running LIRICAL

LIRICAL is a command-line Java tool that runs with Java version 8 or higher. LIRICAL can be run both with and without genomic data in form of a VCF file from genome, exome, or NGS gene-panel sequencing.

To get help, run LIRICAL with a command or with the option “-h”:

$ java -jar target/LIRICAL.jar -h
  Usage: java -jar LIRICAL [-hV] [COMMAND]
  LIkelihood Ratio Interpretation of Clinical AbnormaLities
    -h, --help      Show this help message and exit.
    -V, --version   Print version information and exit.
  Commands:
    download, D     Download files for LIRICAL
    phenopacket, P  Run LIRICAL from a Phenopacket
    yaml, Y         Run LIRICAL from YAML file

Run LIRICAL with a specific command with the “-h” option to get information about the command, e.g.,

$ java -jar target/LIRICAL.jar download -h
  Usage: java -jar LIRICAL download [-hVw] [-d=<datadir>]
  Download files for LIRICAL
    -d, --data=<datadir>   directory to download data (default: data)
    -h, --help             Show this help message and exit.
    -V, --version          Print version information and exit.
    -w, --overwrite        overwrite previously downloaded files (default: false)

LIRICAL has three main commands, download, phenopacket, and yaml. The download command needs to be run before anything else and downloads some files required for LIRICAL analysis. LIRICAL can then be run using a Phenopacket or a YAML-formated file as input.

Running LIRICAL with a Phenopacket

LIRICAL can be run with clinical data (HPO terms) only or with clinical data and a VCF file representing the results of gene panel, exome, or genome sequencing. The prefered input format is Phenopackets, an open standard for sharing disease and phenotype information. This is a new standard of the Global Alliance for Genomics and Health that links detailed phenotype descriptions with disease, patient, and genetic information.

PhenopacketGenerator

For convenience, we provide a tool called PhenopacketGenerator that can be used to create a Phenopacket with a list of HPO terms and the path to a VCF file with which LIRICAL can be run.

Running LIRICAL with a YAML file

The other allowed input format is YAML. The format is designed to be as close as possible to that of the Exomiser YAML format, but some fields, such as negated HPO terms, as LIRICAL-specific.

Choosing between YAML and Phenopacket input formats

How should users choose between YAML and Phenopackets as an input format?