I'm running VEP version 85 in offline mode, but I wasn't asked to download any database for GO.
I'm using the GO.pm plugin in my command-line, but the GO column is completely empty. The Clinvar column is not empty, and I didn't have to download anything for that either, so I'm not sure what I'm missing.
What does GO.pm need to work?
Hello,
The VEP GO.pm requires a database connection: https://github.com/Ensembl/VEP_plugins/blob/release/87/GO.pm
Try using --database, rather than --cache.
Best wishes
Ben Ensembl Helpdesk
Helo Ben, I am trying to link GO and VEP but it does not produce any output from GO.
**vep -i vcf_file.vcf --database --refseq --port 3337 --plugin GO,MF --fasta ../../referencia/hg19.fa --force_overwrite
** Also I have tried.
vep -i vcf_file.vcf --database --refseq --port 3337 --plugin GO --fasta ../../referencia/hg19.fa --force_overwrite
What I am doing wrong ?
Hi Edmond,
You are using the RefSeq transcript set but the VEP GO plugin only retrieves Gene Ontology terms associated with Ensembl transcripts/translations using the Ensembl Perl API: https://github.com/Ensembl/VEP_plugins/blob/release/104/GO.pm
Best wishes
Ben
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