Ensembl Tools

We provide a number of ready-made tools for processing both our data and yours. We routinely delete results from our servers after 10 days, but if you have an ensembl account you will be able to save the results indefinitely.

Processing your data

Name	Description	Online tool	Upload limit	Download script	Documentation
Variant Effect Predictor	Analyse your own variants and predict the functional consequences of known and unknown variants via our Variant Effect Predictor (VEP) tool.		50MB*
Variant Recoder	Translate a variant identifier, HGVS notation or genomic SPDI notation to all possible variant IDs, HGVS, VCF format and genomic SPDI.		Maximun 1000 variants recommended
BLAST/BLAT	Search our genomes for your DNA or protein sequence.		50MB
File Chameleon	Convert Ensembl files for use with other analysis tools
Assembly Converter	Map (liftover) your data's coordinates to the current assembly.		50MB
ID History Converter	Convert a set of Ensembl IDs from a previous release into their current equivalents.		50MB
Linkage Disequilibrium Calculator	Calculate LD between variants using genotypes from a selected population.
Allele frequency calculator	This tool calculates population-wide allele frequency for sites within the chromosomal region defined from a VCF file and populations defined in a sample panel file.
VCF to PED converter	Parse a vcf file to create a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview.
Data Slicer	Get a subset of data from a BAM or VCF file.
Variation Pattern Finder	Identify variation patterns in a chromosomal region of interest for different individuals. Only variations with functional significance such non-synonymous coding, splice site will be reported by the tool.

* For larger datasets we provide an API script that can be downloaded (you will also need to install our Perl API, below, to run the script).

Accessing Ensembl data

Name	Description	Get it from:	Documentation
BioMart	Use this data-mining tool to export custom datasets from Ensembl.	Ensembl Biomart
Ensembl Perl API	Programmatic access to all Ensembl data using simple Perl scripts	GitHub or FTP download (current release only)
Ensembl Virtual Machine	VirtualBox virtual Machine with Ubuntu desktop and pre-configured with the latest Ensembl API plus Variant Effect Predictor (VEP). NB: download is >1 GB	FTP download
Ensembl REST server	Access Ensembl data using your favourite programming language	grch37.rest.ensembl.org