search

TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
Other
22 stars 11 forks source link

no gene in entrezGeneId #635

Closed Chahdilm closed 7 months ago

Chahdilm commented 7 months ago

Hello, I have an issu there is no gene in the colunm "entrezGeneId". This is the process i did: I use the last version of LIRICAL : v2.0.0-RC2. I download the datafile folder : java -jar lirical-cli-2.0.0-RC2.jar download -d datafiles --overwrite I use this command on the LDS2.v2.json file in the example folder : I want to use LIRICAL only on HPO i don't need variants info. (so no need to download hg19 or hg38 from exomiser Am i correct ?) java -jar lirical-cli-2.0.0-RC2.jar phenopacket -p examples/LDS2.v2.json -d datafiles/ -f tsv --use-orphanet -x v1

This is the tsv output : image

If needed this is what my folder look like: image

I want to understand why i have no gene for the diseases in the output. Is there something wrong on my process ? Thank you !

ielis commented 7 months ago

Hi @Chahdilm

no, I think your setup is OK.

want to use LIRICAL only on HPO i don't need variants info. (so no need to download hg19 or hg38 from exomiser Am i correct ?)

Yes, for the phenotype-only mode you do not need to download the exomiser database files.

I want to understand why i have no gene for the diseases in the output. Is there something wrong on my process ?

No, your setup/process seems OK and not having gene ids and variants is normal for phenotype-only results. In fact, presence of the entrezGeneId and variants columns is a shortcoming from our side; the columns are there because under the hood we use the same template for reporting results from both phenotype-only and variant-aware analyses. The columns contain data when variant-aware analysis is run.

Chahdilm commented 7 months ago

Thank you for responding promptly !