search

Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
170 stars 44 forks source link

Gene referenced in transcript not present in genes section #77

Open olingerc opened 2 years ago

olingerc commented 2 years ago

I regularly have transcripts with a "hgnc" value but I can not find the corresponding gene in the genes section at the end of the json file. Could you give a few details about the criteria used to include a gene?

This is a sentence from the Nirvana main website:

For each gene that was referenced in the transcripts found in the positions section, there will be additional gene-level annotation in the gene section.

rajatshuvro commented 2 years ago

Hi @olingerc , currently, if a gene only has upstream or downstream variants, it is not represented in the genes section. So far none of our users have asked for them. But if you have a use case, please let us know and we will consider it.

Regards Rajat

olingerc commented 2 years ago

Thanks @rajatshuvro . That makes a lot of sense. I can accept this behavior. Maybe a small notice in the documentation could help here?