command line VEP and VEP web interface return different results.

Question

[nhaus]

I am trying to predict the consequence of a handful of germline mutations, and I realized, that the Consequence field differs if I use the web interface vs my local command line installment.

I am using ensembl-vep : 104.0 and this is the exact command:

./vep -input_data "rs10437082"  -o stdout --database --assembly "GRCh37" --no_stats

It predicts the consequence as intergenic_variant. However, if I look up the variant on ensembl webpage, it says that it is a regulatory region variant. If I run instant VEP on the VEP webtool, it also says that it is a regulatory region variant.

I would appreciate any insights to why I am observing the discrepancies!

Answer 1

[Emily]

The option --regulatory, which gives you the consequences on regulatory regions, is not enabled by default on the command line tool. Docs