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

NameDescriptionOnline toolUpload limitDownload scriptDocumentation
Variant Effect Predictor
Analyse your own variants and predict the functional consequences of known and unknown variants via our Variant Effect Predictor (VEP) tool.Tool50MB*DownloadDocumentation
Variant RecoderTranslate a variant identifier, HGVS notation or genomic SPDI notation to all possible variant IDs, HGVS, VCF format and genomic SPDI.ToolMaximun 1000 variants recommendedDownloadDocumentation
BLAST/BLATSearch our genomes for your DNA or protein sequence.Tool50MBDocumentation
File ChameleonConvert Ensembl files for use with other analysis toolsToolDownloadDocumentation
Assembly ConverterMap (liftover) your data's coordinates to the current assembly.Tool50MBDocumentation
ID History ConverterConvert a set of Ensembl IDs from a previous release into their current equivalents.Tool50MBDownloadDocumentation
Linkage Disequilibrium CalculatorCalculate LD between variants using genotypes from a selected population.ToolDocumentation
Allele frequency calculatorThis 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.ToolDownloadDocumentation
VCF to PED converterParse 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.ToolDownloadDocumentation
Data SlicerGet a subset of data from a BAM or VCF file.ToolDocumentation
Variation Pattern FinderIdentify 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.ToolDownloadDocumentation
* 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

NameDescriptionGet it from:Documentation
BioMartUse this data-mining tool to export custom datasets from Ensembl.Ensembl BiomartDocumentation
Ensembl Perl APIProgrammatic access to all Ensembl data using simple Perl scriptsGitHub or FTP download (current release only)Documentation
Ensembl Virtual MachineVirtualBox virtual Machine with Ubuntu desktop and pre-configured with the latest Ensembl API plus Variant Effect Predictor (VEP). NB: download is >1 GBFTP downloadDocumentation
Ensembl REST serverAccess Ensembl data using your favourite programming languagegrch37.rest.ensembl.orgDocumentation