This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tool: Ensembl Vep - Variant Effect Predictor

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:

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.

snp variant-annotation
• 5,582 views • link
updated by gernophil • gernophil • written by Malachi Griffith Malachi Griffith

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

• 1 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

2 answers

I have a SNP file in vcf format with just 2000 SNPs of a bacteria. But the species option in the input doesn't allow me to choose the right one. And the maximum SNPs shouldn't be more than 750 I guess otherwise the vcf file need to be splited. Any other way I can use by SNPs file from my bacteria not listed in the species option?

• 0 views • link
written by bioinfo bioinfo

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.

• 1 views • link
written by deepti24shine • deepti24shine

Log in to answer this question.

More posts like this