Tool:Ensembl Vep - Variant Effect Predictor

Question

[Malachi Griffith]

Ensembl provides the facility to predict the functional consequences of known and unknown variants using the Variant Effect Predictor (VEP). There are three primary ways to use the functionality of the VEP:

• Through the web interface
• Using the standalone perl script
• Using Ensembl's perl API

The web version is suitable for users with small volumes of data or those who prefer not to use command-line utilities. The script version is the most flexible of the VEP, and allows users to process large volumes of data using their own compute resources. The API is suitable for perl programmers looking to incorporate features of the VEP into their own code.

[Giovanni M Dall'Olio]

I wonder if there is any standard way to install this script. For example a .deb, .rpm, or via linuxbrew.

Answer 1

[deepti24shine]

Helllo malachig,

Thanks to share such information.I got something very informative about VEP and API..and will try to work out for my purpose...

i just want to know how to get whole data about the particular gene,like exon, intron, UTR region, transcription start site,promoter site, start codons, stop codons etc and also how to get sequence of desired mutation site... I am a new user of biostar..and trying to fulfill my queries through this site.. thanking u.

[Laura]

If you wish to get gene structures I would recommend you look at the Ensembl Core API tutorial

http://www.ensembl.org/info/docs/api/core/core_tutorial.html