YAML input format

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

LIRICAL uses default values for many configuration options, and a simple YAML configuration file would include the following information:

## LIRICAL Analysis Template.
# These are all the possible options for running LIRICAL. Use this as a template for your own set-up.
---
sampleId: NF2-example
hpoIds: ['HP:0002321', 'HP:0000365', 'HP:0000360', 'HP:0009589', 'HP:0002858']
negatedHpoIds: ['HP:0009736']
age: P20Y6M
sex: FEMALE
vcf: /path/to/example.vcf

In YAML, lines that begin with # are comments, and the three dashes indicate the start of the contents of the file.

  1. sampleId is the identifier of the individual being analyzed.

  2. hpoIds is a list of HPO term representing the clinical manifestations observed in the individual being analyzed.

  3. negatedHpoIds a list of HPO terms that represent abnormalities that were excluded in the proband.

  4. age age of the individual entered using the ISO8601 duration notation. E.g. P20Y6M for an individual with age of 20 years and 6 months.

  5. sex sex of the individual, either MALE or FEMALE.

  6. vcf is the path to the file we want to analyze. Note that the VCF file must contain the sample corresponding to sampleId and the CLI must include --assembly and -ed19 | -ed38 options to leverage the VCF file

to run a genotype-aware analysis.

You can use the example file as a starting point for your own configuration file. An example YAML file can also be found in the examples folder.