Unable to parse HGVS notation about ensembl-vep HOT 2 CLOSED

You must specify either --database (to use the database only), --cache (to primarily use the cache but allow database connections) or --offline (use the cache only, forbid database connections). VEP should warn you of this before it attempts to parse the HGVS input, so I'm surprised you got the error you saw.

So your first command should be:

perl /usr/local/ensembl-vep/vep.pl -i test_HGVS-annotation.txt --database

OR

perl /usr/local/ensembl-vep/vep.pl -i test_HGVS-annotation.txt --cache

And your second example should be:

perl /usr/local/ensembl-vep/vep.pl -i /usr/local/ensembl-vep/examples/homo_sapiens_GRCh37.vcf -o ~/test2 --cache

NB --offline will not work with HGVS input.

from ensembl-vep.

Wow I'm sorry I missed the --database argument. Thank's for the fast response, it's working smoothly now.

from ensembl-vep.