Running LIRICAL with a YAML file (HPO data)

The recommended input format for running LIRICAL is the Phenopacket, but LIRICAL also supports YAML, which is a simple, human readable format that is commonly used for configuration files.

YAML

Before running LIRICAL, download and built it and set it up according to the instructions on the Setting up LIRICAL page. LIRICAL uses default values for many configuration options (see below). An example of the simplest possible YAML configuration file is shown:

---
analysis:
  # hg19 or hg38 is supported
  genomeAssembly: hg19
hpoIds: ['HP:0001156', 'HP:0001363', 'HP:0011304', 'HP:0010055']

This file can be found at src/test/resources/yaml/simple.yml.

An example YAML file that uses several parameters is shown below:

## LIRICAL Analysis Template.
# These are all the possible options for running LIRICAL. Use this as a template for
# your own set-up.
---
analysis:
# hg19 or hg38 is supported
    mindiff: 50
    threshold: 0.05
    tsv: false
    datadir: data
    orphanet: false
hpoIds: ['HP:0001156', 'HP:0001363', 'HP:0011304', 'HP:0010055']
negatedHpoIds: ['HP:0001328']
prefix: example
outdir: /path/to/output/directory

This file can be found at src/test/resources/yaml/multiple_params.yml.

In YAML, lines that begin with # are comments, and the three dashes indicate the start of the contents of the file. The analysis element is used to hold a dictionary with options for running the program. The items in analysis refer to the genome assembly and to the paths of files required to run LIRICAL. Users must provide values for genomeAssembly, vcf, and exomiser. Default values will be use for the other three entries if the user does not provide values.

1. mindiff By default, LIRICAL shows all differential diagnoses with a posterior probability of at least 1%, and at least 10 entries regardless of the posterior probability. If you want LIRICAL to show details about more differentials, set this option to the desired number.

2. threshold This option controls the minimum post-test probability to show a differential diagnosis in HTML output. By default, LIRICAL shows all differnetials with a posterior probability of 1% or greater.

3. tsv Use TSV instead of HTML output (Default: false).

4. datadir The path with LIRICAL data that should be downloaded before running LIRICAL (see Setting up LIRICAL for details). This option should not be used if the default data location (data) is used.

5. orphanet If true, use annotation data from Orphanet.

Additionally, hpoIds is a list of HPO term representing the clinical manifestations observed in the individual being analyzed. In contrast, negatedHpoIds represents phenotypic abnormalities (HPO terms) that were explicitly excluded in the proband.

Finally, prefix is the prefix of the output file (optional, default: lirical). For instance, if the prefix is example1, then the HTML output file will be example1.html.

Running LIRICAL

A typical command that runs LIRICAL using settings shown in the YAML file with the default data directory would be simply

$ java -jar LIRICAL.jar yaml -y example.yml