LIRICAL TSV Output¶
If LIRICAL is run with the --tsv option, it will output a tab-separated values (TSV) file with the results for each of the
diagnoses. For example, the following command will run LIRICAL on a Phenopacket and output a TSV file with the results.
$ java -jar LIRICAL.jar phenopacket \
--global \
-e /path(..)/1811_hg19 \
-p /path(..)/example-phenopacket.json \
--tsv
By default, LIRICAL outputs the data to a file called lirical.tsv. This can be altered with the -x <prefix> option.
| Item | Explanation |
|---|---|
| rank | placement of the candidate diagnosis by LIRICAL |
| diseaseName | Name of the candidate disease |
| diseaseCurie | disease ID, e.g., OMIM:154700 |
| pretestprob | Pretest probability of the candidate disease |
| postestprob | Postest probability of the candidate disease |
| compositeLR | Combined likelihood ratio of the candidate disease (logarithm of the product of all individual LRs) |
| entrezGeneId | Identifier of the candidate disease gene (if available) |
| variants | variant evaluation (if available) |
The file begins with comment lines (that start with an exclamation mark) that provide information about the HPO terms used to run the analysis.