How do I get GO term annotations using VEP?

Question

[anp375]

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?

Answer 1

[Ben Moore]

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

[Edmond]

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 ?

[Ben Moore]

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