LIRICAL: LIkelihood Ratio Interpretation of Clinical AbnormaLities

LIRICAL

This application performs phenotype-driven prioritization of candidate diseases and genes in the setting of genomic diagnostics (exome or genome) in which the phenotypic abnormalities are described as Human Phenotype Ontology (HPO) terms.

Contents:

• Setting up LIRICAL
  • Prerequisites
  • Prebuilt LIRICAL executable
  • Building from sources
  • Building to use as a library
  • Set up alias
  • Exomiser database files
  • LIRICAL data files
• Tutorial
  • Setup
  • The data
  • Creating a phenopacket
  • Running LIRICAL
  • Viewing the results
• Running LIRICAL
  • Shared CLI options
  • LIRICAL prioritization commands
  • Choosing between YAML and Phenopacket input formats
• Analysis input validation
  • Analysis requirements
  • Validation policy
• Output files
  • LIRICAL HTML output
  • LIRICAL TSV output
  • LIRICAL JSON output
• LIRICAL: How does it work?
  • LIRICAL’s Phenotype Score
  • LIRICAL’s Genotype Score
• LIRICAL Advanced Options
  • Generating the background files