LIRICAL Options¶
This page summarizes the options explained in detail in the Running LIRICAL section.
Download¶
The download command downloads files required to run LIRICAL:
- Homo_sampiens_gene_info.gz
- hp.obo
- phenotype.hpoa
- mim2gene_medgen
By default, LIRICAL will create a directory called data and download the files there. LIRICAL will
download to a non-default directory if the user passes the -d option.
| short | long | Default | Explanation |
|---|---|---|---|
-d |
--download |
data | directory to download data |
-w |
--overwrite |
false | overwrite prevously downloaded files, if any |
Running LIRICAL with a phenopacket¶
The phenopacket command runs LIRICAL from a Phenopacket file.
| short | long | Default | Explanation |
|---|---|---|---|
-p |
--phenopacket |
n/a | path to Phenopacket |
-d |
--download |
data | diretory that contains the downloaded data |
-g |
--global |
false | retain candidate diseases even if no candidate gene is known or no candidate variant is found in VCF file. |
-m |
--mindiff |
10 | minimal number of differential diagnoses to show in the HTML output file. |
-o |
--output-directory |
n/a | directory into which to write output file(s). |
-x |
--prefix |
lirical | prefix of outfile |
-t |
--threshold |
0.01 | minimum post-test probability to show a diagnosis in the HTML output. This option, together with --mindiff, controls the number of panels that show information about candidates in the HTML output. |
| none | --transcriptdb |
ucsc | transcript database. Valid options are UCSC, Ensembl, and RefSeq |
| none | --tsv |
false | Use TSV instead of HTML output |
YAML¶
The yaml command runs LIRICAL from a YAML configuration file. Users should
indicate all non-default arguments within the YAML file. The only valid argument for the
yaml command is the path to the YAML file (-y <path>).
$ java -jar LIRICAL.java yaml -y example.yaml
| short | long | Default | Explanation |
|---|---|---|---|
-y |
--yaml |
n/a | path to yaml configuration file |