Ensembl Rest API - GET vep/:species/id/:id

<!DOCTYPE html> <html lang="en"> <head> <script src="/static/js/20-prettify.js"></script> <script src="/static/js/30-jquery-1.11.1.min.js"></script> <script src="/static/js/highlight/highlight.pack.js"></script> <meta charset="utf-8"/> <meta name="viewport" content="width=device-width, initial-scale=1.0"/> <title>Ensembl Rest API - GET vep/:species/id/:id</title> <link href='/_asset/8f35166051019d4c43cb29867ae6f94a.css' rel='stylesheet'/> <style> body { padding-top: 60px; /* 60px to make the container go all the way to the bottom of the topbar */ } </style> <link href="/static/css/premin/bootstrap-responsive.min.css" rel="stylesheet">   </head> <body data-spy="scroll" data-target=".bs-docs-sidebar" onload="prettyPrint()"> <div class="container"> <div class="navbar navbar-inverse navbar-fixed-top"> <div class="navbar-inner"> <div class="container"> <a class="brand" href="http://www.ensembl.org"><img class="brand" src="/static/img/e-ensembl.png" alt="Service logo"/></a> <ul class="nav"> <li class="active"><a href="/">Endpoints</a></li> <li><a href="http://github.com/Ensembl/ensembl-rest/wiki">User Guide</a></li> <li><a href="http://github.com/Ensembl/ensembl-rest/wiki/Change-log">Change Log</a></li> <li><a href="http://www.ensembl.org/info/about/index.html">About the Ensembl Project</a></li> <li><a href="http://www.ensembl.org/info/about/contact/">Contact Ensembl</a></li> <li><a target="_blank" href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice">Privacy Notice</a></li> </ul> </div> </div> </div> <br> <span class="message"></span> <span class="error"></span> <h1 id="title">GET vep/:species/id/:id</h1> <div class="row"> <div class="span10"> <div class="lead"> <p>Fetch variant consequences based on a variant identifier</p> </div> <h2>Parameters</h2> <h3>Required</h3> <table class="table table-striped"> <thead> <tr> <th>Name</th><th>Type</th><th>Description</th><th>Default</th><th>Example Values</th> </tr> </thead> <tbody> <tr> <td> id </td> <td><var>String</var></td> <td>Query ID. Supports dbSNP, COSMIC and HGMD identifiers, including structural variant idefentifiers.</td> <td><var> - </var></td> <td> <var>rs56116432</var><br> <var>COSM476</var><br> <var>__VAR(sv_id)__</var><br> </td> </tr> <tr> <td> species </td> <td><var>String</var></td> <td>Species name/alias</td> <td><var> - </var></td> <td> <var>homo_sapiens</var><br> <var>human</var><br> </td> </tr> </tbody> </table> <h3>Optional</h3> <table class="table table-striped"> <thead> <tr> <th>Name</th><th>Type</th><th>Description</th><th>Default</th><th>Example Values</th> </tr> </thead> <tbody> <tr> <td> AlphaMissense </td> <td><var>Boolean</var></td> <td>Annotates missense variants with the pre-computed <a target="_blank" href="https://www.science.org/doi/10.1126/science.adg7492">AlphaMissense</a> pathogenicity scores. AlphaMissense is a deep learning model developed by Google DeepMind that predicts the pathogenicity of single nucleotide missense variants. Data contained within the AlphaMissense Database is licensed under the Creative Commons Attribution 4.0 International License (CC-BY) (the "License"). You may obtain a copy of the License at: <a target="_blank" href="https://creativecommons.org/licenses/by/4.0/legalcode">https://creativecommons.org/licenses/by/4.0/legalcode</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/AlphaMissense.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> AncestralAllele </td> <td><var>Boolean</var></td> <td>Retrieves the ancestral allele for variants inferred from the Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/AncestralAllele.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> Blosum62 </td> <td><var>Boolean</var></td> <td>Include BLOSUM62 amino acid conservation score (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Blosum62.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> CADD </td> <td><var>Boolean</var></td> <td>Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants (also supports sus_scrofa), indels and structural variants (only supported in GRCh38). Following options can be given: <b>snv</b>, <b>indels</b>, <b>snv_indels</b>, and <b>sv</b>. Providing 1 is also supported which is same as providing <b>snv_indels</b>. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made. See <a target="_blank" href="https://cadd.gs.washington.edu/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/CADD.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>snv_indels,<wbr>1</var><br> </td> </tr> <tr> <td> ClinPred </td> <td><var>Boolean</var></td> <td><a rel="external" href="https://sites.google.com/site/clinpred">ClinPred</a> is a prediction tool to identify disease-relevant nonsynonymous single nucleotide variants (only supported for human). The predictor incorporates existing pathogenicity scores and benefits from normal population allele frequencies. ClinPred is only available for non-commercial use. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/ClinPred.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> Conservation </td> <td><var>Boolean</var></td> <td>Retrieves a conservation score from the Ensembl Compara databases for variant positions (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Conservation.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> DisGeNET </td> <td><var>Boolean</var></td> <td>Retrieves Variant-Disease-PMID associations from the DisGeNET database (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DisGeNET.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> DosageSensitivity </td> <td><var>Boolean</var></td> <td>Retrieves haploinsufficiency and triplosensitivity probability scores for affected genes from a published <a target="_blank" href="https://www.sciencedirect.com/science/article/pii/S0092867422007887">dosage sensitivity catalogue</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DosageSensitivity.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> EVE </td> <td><var>Boolean</var></td> <td>EVE (evolutionary model of variant effect) is a computational method for the classification of human genetic variants trained solely on evolutionary sequences. See <a target="_blank" href="https://evemodel.org/">license</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/EVE.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> Enformer </td> <td><var>Boolean</var></td> <td>Predictions of variant impact on gene expression</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> GO </td> <td><var>Boolean</var></td> <td>Retrieves Gene Ontology terms associated with transcripts/translations</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> GeneSplicer </td> <td><var>Boolean</var></td> <td>Detects splice sites in genomic DNA (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/GeneSplicer.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> Geno2MP </td> <td><var>Boolean</var></td> <td>Geno2MP is a web-accessible database of rare variant genotypes linked to individual-level phenotypic profiles defined by human phenotype ontology (HPO) terms (<a target="_blank" href="https://raw.githubusercontent.com/Ensembl/VEP_plugins/main/Geno2MP.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> IntAct </td> <td><var>Boolean</var></td> <td>Provides molecular interaction data for variants as reported by <a target="_blank" href="https://www.ebi.ac.uk/intact/home">IntAct</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/IntAct.pm">plugin details</a>)</td> <td><var> - </var></td> <td> <var>-</var> </td> </tr> <tr> <td> LOEUF </td> <td><var>Boolean</var></td> <td>Adds LOEUF (loss-of-function observed/expected upper bound fraction) constraint scores derived from gnomAD. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/LOEUF.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> LoF </td> <td><var>Boolean</var></td> <td>LOFTEE identifies LoF (loss-of-function) variation. See <a target="_blank" href="https://github.com/konradjk/loftee/blob/master/README.md">README</a> for more details.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> Mastermind </td> <td><var>Boolean</var></td> <td>Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> MaveDB </td> <td><var>Boolean</var></td> <td>Provides scores from Multiplexed Assays of Variant Effect for variants as reported by <a target="_blank" href="https://www.mavedb.org">MaveDB</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaveDB.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> MaxEntScan </td> <td><var>Boolean</var></td> <td>Sequence motif and maximum entropy based splice site consensus predictions (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/MaxEntScan.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> NMD </td> <td><var>Boolean</var></td> <td>Predicts if a variant allows the transcript escape nonsense-mediated mRNA decay. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/NMD.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> OpenTargets </td> <td><var>Boolean</var></td> <td>Reports locus-to-gene (L2G) scores to predict causal genes at GWAS loci from <a target="_blank" href="https://genetics.opentargets.org">Open Targets Genetics</a>. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/OpenTargets.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> Phenotypes </td> <td><var>Boolean</var></td> <td>Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> REVEL </td> <td><var>Boolean</var></td> <td><a rel="external" href="https://sites.google.com/site/revelgenomics">Rare Exome Variant Ensemble Learner (REVEL)</a> is an ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from multiple individual tools. REVEL is only available for non-commercial use. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/REVEL.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> RiboseqORFs </td> <td><var>Boolean</var></td> <td>Calculates consequences for variants overlapping <a target="_blank" href="https://doi.org/10.1038/s41587-022-01369-0">Ribo-seq ORFs</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/RiboseqORFs.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> SpliceAI </td> <td><var>Integer</var></td> <td>Retrieves pre-calculated annotations from SpliceAI a deep neural network, developed by Illumina, Inc that predicts splice junctions from an arbitrary pre-mRNA transcript sequence. Used for non-commercial purposes. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/SpliceAI.pm">plugin details</a>) <br>The pre-calculated annotations for all possible single nucleotide substitutions can be retrieved from: value <b>1</b>) Ensembl/GENCODE v24 canonical transcripts (masked scores); value <b>2</b>) Ensembl/GENCODE v37 MANE transcripts (raw scores). <br>Note: The pre-calculated annotations for 1 base insertions, and 1-4 base deletions are only available for Ensembl/GENCODE v24 canonical transcripts.</td> <td><var> 0 </var></td> <td> <var>2</var><br> </td> </tr> <tr> <td> UTRAnnotator </td> <td><var>Boolean</var></td> <td>Annotates high-impact five prime UTR variants either creating new upstream ORFs or disrupting existing upstream ORFs (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/UTRAnnotator.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> appris </td> <td><var>Boolean</var></td> <td>Include APPRIS isoform annotation</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> callback </td> <td><var>String</var></td> <td>Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see <a href="http://github.com/Ensembl/ensembl-rest/wiki">the user guide</a>.</td> <td><var> - </var></td> <td> <var>randomlygeneratedname</var><br> </td> </tr> <tr> <td> canonical </td> <td><var>Boolean</var></td> <td>Include a flag indicating the canonical transcript for a gene</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> ccds </td> <td><var>Boolean</var></td> <td>Include CCDS transcript identifiers</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> dbNSFP </td> <td><var>String</var></td> <td>Comma-separated list of fields from dbNSFP, a database of pathogenicity predictions for missense variants. See <a target="_blank" href="https://usf.box.com/s/h9mqovab0on1r3hpopwypcjr9i9mf0s3">dbNSFP README</a> for field list or include all fields with <code>ALL</code>; this fetches a large amount of data per variant! By default, some fields contain values for all Ensembl transcripts; add <code>transcript_match=1</code> to only return values for the matched Ensembl transcript. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/dbNSFP.pm">plugin details</a>)</td> <td><var> Not used </var></td> <td> <var>LRT_pred,<wbr>MutationTaster_pred</var><br> </td> </tr> <tr> <td> dbscSNV </td> <td><var>Boolean</var></td> <td>Predictions for splicing variants from dbscSNV. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/dbscSNV.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> distance </td> <td><var>Integer</var></td> <td>Change the distance to transcript for which VEP assigns upstream and downstream consequences</td> <td><var> 5000 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> domains </td> <td><var>Boolean</var></td> <td>Include names of overlapping protein domains</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> failed </td> <td><var>Boolean</var></td> <td>When checking for co-located variants, by default variants flagged as failed by Ensembl's QC pipeline will be excluded. Set this flag to 1 to include such variants</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> flag_pick </td> <td><var>Boolean</var></td> <td>As per <b>pick</b>, but adds the PICK flag to the chosen block of consequence data and retains others.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> flag_pick_allele </td> <td><var>Boolean</var></td> <td>As per <b>pick_allele</b>, but adds the PICK flag to the chosen block of consequence data and retains others.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> flag_pick_allele_gene </td> <td><var>Boolean</var></td> <td>As per <b>pick_allele_gene</b>, but adds the PICK flag to the chosen block of consequence data and retains others.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> ga4gh_vrs </td> <td><var>Boolean</var></td> <td>Add GA4GH Variation Representation Specification (VRS) notation</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> gencode_basic </td> <td><var>Boolean</var></td> <td>Limit your analysis to transcripts belonging to the GENCODE basic set. This set has fragmented or problematic transcripts removed.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> gencode_primary </td> <td><var>Boolean(0,1)</var></td> <td>Limit your analysis to transcripts belonging to the GENCODE primary set.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> hgvs </td> <td><var>Boolean</var></td> <td>Include HGVS nomenclature based on Ensembl stable identifiers</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> mane </td> <td><var>Boolean</var></td> <td>Include MANE Select annotations (GRCh38 only)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> merged </td> <td><var>Boolean</var></td> <td>Use merged Ensembl and RefSeq transcript set to report consequences (human only)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> minimal </td> <td><var>Boolean</var></td> <td>Convert alleles to their most minimal representation before consequence calculation i.e. sequence that is identical between each pair of reference and alternate alleles is trimmed off from both ends, with coordinates adjusted accordingly. Note this may lead to discrepancies between input coordinates and coordinates reported by VEP relative to transcript sequences</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> mirna </td> <td><var>Boolean</var></td> <td>Determines where in the secondary structure of a miRNA a variant falls</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> mutfunc </td> <td><var>Boolean</var></td> <td>Predicts destabilization effect of protein structure, interaction, regulatory region etc. caused by a variant as reported by <a target="_blank" href="http://www.mutfunc.com/">mutfunc</a> database. (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/mutfunc.pm">plugin details</a>)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> numbers </td> <td><var>Boolean</var></td> <td>Include affected exon and intron positions within the transcript</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> per_gene </td> <td><var>Boolean</var></td> <td>Output only the most severe consequence per gene. The transcript selected is arbitrary if more than one has the same predicted consequence. Uses the same ranking system as <b>pick</b>.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> pick </td> <td><var>Boolean</var></td> <td>Pick one line or block of consequence data per variant, including transcript-specific columns. Consequences are chosen according to the criteria described <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick">here</a>, and the order the criteria are applied may be customised with <b>pick_order</b>. This is the best method to use if you are interested only in one consequence per variant.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> pick_allele </td> <td><var>Boolean</var></td> <td>Like <b>pick</b>, but chooses one line or block of consequence data per variant allele. Will only differ in behaviour from <b>pick</b> when the input variant has multiple alternate alleles.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> pick_allele_gene </td> <td><var>Boolean</var></td> <td>Like <b>pick_allele</b>, but chooses one line or block of consequence data per variant allele and gene combination.</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> pick_order </td> <td><var>String</var></td> <td>Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane_select mane_clinical ].</td> <td><var> mane_select,<wbr>mane_clinical,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length </var></td> <td> <var>-</var> </td> </tr> <tr> <td> protein </td> <td><var>Boolean</var></td> <td>Include Ensembl protein identifiers</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> refseq </td> <td><var>Boolean</var></td> <td>Use RefSeq transcript set to report consequences (human only)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> shift_3prime </td> <td><var>Boolean</var></td> <td>Shift transcript-overlapping variants as far as possible in the 3' direction before providing consequences</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> shift_genomic </td> <td><var>Boolean</var></td> <td>Shift all variants as far as possible in the 3' direction before providing consequences</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> transcript_id </td> <td><var>String</var></td> <td>Filter results by Transcript ID</td> <td><var> Not Used </var></td> <td> <var>-</var> </td> </tr> <tr> <td> transcript_version </td> <td><var>Boolean</var></td> <td>Add version numbers to Ensembl transcript identifiers</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> tsl </td> <td><var>Boolean</var></td> <td>Include transcript support level (TSL) annotation</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> uniprot </td> <td><var>Boolean</var></td> <td>Include best match accessions for translated protein products from three UniProt-related databases (SWISSPROT, TREMBL and UniParc)</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> variant_class </td> <td><var>Boolean</var></td> <td>Output the Sequence Ontology variant class for the input variant</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> vcf_string </td> <td><var>Boolean</var></td> <td>Include alleles in VCF format</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> <tr> <td> xref_refseq </td> <td><var>Boolean</var></td> <td>Include aligned RefSeq mRNA identifiers for transcript. NB: theRefSeq and Ensembl transcripts aligned in this way MAY NOT, AND FREQUENTLY WILL NOT, match exactly in sequence, exon structure and protein product</td> <td><var> 0 </var></td> <td> <var>-</var> </td> </tr> </tbody> </table> <h2>Example Requests</h2> <h3><a href="/vep/human/id/COSM476?content-type=application/json">/vep/human/id/COSM476?content-type=application/json</a></h3> <br> <ul class="nav nav-pills"> <li class="active"><a href="#examplecosmic" data-toggle="tab">Example output</a></li> <li><a href="#perlcosmic" data-toggle="tab">Perl</a></li> <li><a href="#python2cosmic" data-toggle="tab">Python2</a></li> <li><a href="#python3cosmic" data-toggle="tab">Python3</a></li> <li><a href="#rubycosmic" data-toggle="tab">Ruby</a></li> <li><a href="#javacosmic" data-toggle="tab">Java</a></li> <li><a href="#rcosmic" data-toggle="tab">R</a></li> <li><a href="#curlcosmic" data-toggle="tab">Curl</a></li> <li><a href="#wgetcosmic" data-toggle="tab">Wget</a></li> </ul> <div class='tab-content'> <div class='tab-pane active' id='examplecosmic'></div>  <script> var method = "GET"; var params = { url : "/vep/human/id/COSM476?content-type=application/json", type : method, beforeSend : function () { $("#examplecosmic").append("<img src='/static/img/e-loader.gif'>"); return true; }, success : function (resp) { // If it has a documentElement we assume it is xml if (resp.documentElement == undefined) { if (typeof (resp) === "string") { $("#examplecosmic").append("<pre class=\"pre-scrollable\"> <code class=\"json\">" + resp + "</code></pre>"); $("#examplecosmic").each (function (i, block) { $("#examplecosmic>img").remove(); }) } else { var json = JSON.stringify(resp, undefined, 2); $("#examplecosmic").append("<pre class=\"pre-scrollable\"> <code class=\"json\">" + json + "</code></pre>") $("#examplecosmic").each (function (i, block) { hljs.highlightBlock(block); $("#examplecosmic>img").remove(); }) } } else { var xmlSerial = new XMLSerializer(); var xml_str = xmlSerial.serializeToString(resp); $("#examplecosmic").append("<pre id=\"precosmic\" class=\"pre-scrollable prettyprint\"></pre>"); $("#precosmic").text(xml_str); $("#examplecosmic").each (function (i, block) { hljs.highlightBlock(block); $("#examplecosmic>img").remove(); }) } }, error : function (resp, msg) { $("#examplecosmic").append("<pre id=\"precosmic\"></pre>"); $("#precosmic").text(resp.responseText); $("#examplecosmic>img").remove(); } }; if(method === "POST") { params.processData = false; params.data = ''; params.contentType = 'application/json'; params.accept = ''; } $.ajax( params); </script>   <div class='tab-pane' id='perlcosmic'> <pre class="pre-scrollable prettyprint linenums"> use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://rest.ensembl.org'; my $ext = '/vep/human/id/COSM476?'; my $response = $http->get($server.$ext, { headers => { 'Content-type' => 'application/json' } }); die "Failed!\n" unless $response->{success}; use JSON; use Data::Dumper; if(length $response->{content}) { my $hash = decode_json($response->{content}); local $Data::Dumper::Terse = 1; local $Data::Dumper::Indent = 1; print Dumper $hash; print "\n"; } </pre> </div>  <div class='tab-pane' id='python2cosmic'> <pre class="pre-scrollable prettyprint linenums"> import requests, sys server = "https://rest.ensembl.org" ext = "/vep/human/id/COSM476?" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print repr(decoded) </pre> </div>  <div class='tab-pane' id='python3cosmic'> <pre class="pre-scrollable prettyprint linenums"> import requests, sys server = "https://rest.ensembl.org" ext = "/vep/human/id/COSM476?" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print(repr(decoded)) </pre> </div>  <div class='tab-pane' id='rubycosmic'> <pre class="pre-scrollable prettyprint linenums"> require 'net/http' require 'uri' server='https://rest.ensembl.org' path = '/vep/human/id/COSM476?' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'}) response = http.request(request) if response.code != "200" puts "Invalid response: #{response.code}" puts response.body exit end require 'rubygems' require 'json' require 'yaml' result = JSON.parse(response.body) puts YAML::dump(result) </pre> </div>  <div class='tab-pane' id='javacosmic'> <pre class="pre-scrollable prettyprint linenums"> import java.net.URL; import java.net.URLConnection; import java.net.HttpURLConnection; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.io.Reader; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://rest.ensembl.org"; String ext = "/vep/human/id/COSM476?"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; httpConnection.setRequestProperty("Content-Type", "application/json"); InputStream response = connection.getInputStream(); int responseCode = httpConnection.getResponseCode(); if(responseCode != 200) { throw new RuntimeException("Response code was not 200. Detected response was "+responseCode); } String output; Reader reader = null; try { reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); StringBuilder builder = new StringBuilder(); char[] buffer = new char[8192]; int read; while ((read = reader.read(buffer, 0, buffer.length)) > 0) { builder.append(buffer, 0, read); } output = builder.toString(); } finally { if (reader != null) try { reader.close(); } catch (IOException logOrIgnore) { logOrIgnore.printStackTrace(); } } System.out.println(output); } } </pre> </div>  <div class='tab-pane' id='rcosmic'> <pre class="pre-scrollable prettyprint linenums"> library(httr) library(jsonlite) library(xml2) server <- "https://rest.ensembl.org" ext <- "/vep/human/id/COSM476?" r <- GET(paste(server, ext, sep = ""), content_type("application/json")) stop_for_status(r) # use this if you get a simple nested list back, otherwise inspect its structure # head(data.frame(t(sapply(content(r),c)))) head(fromJSON(toJSON(content(r)))) </pre> </div>  <div class='tab-pane' id='curlcosmic'> <pre class="pre-scrollable prettyprint linenums"> curl 'https://rest.ensembl.org/vep/human/id/COSM476?' -H 'Content-type:application/json' </pre> </div>  <div class='tab-pane' id='wgetcosmic'> <pre class="pre-scrollable prettyprint linenums"> wget -q --header='Content-type:application/json' 'https://rest.ensembl.org/vep/human/id/COSM476?' -O - </pre> </div> </div> <h3><a href="/vep/human/id/rs56116432?content-type=application/json">/vep/human/id/rs56116432?content-type=application/json</a></h3> <br> <ul class="nav nav-pills"> <li class="active"><a href="#exampleone" data-toggle="tab">Example output</a></li> <li><a href="#perlone" data-toggle="tab">Perl</a></li> <li><a href="#python2one" data-toggle="tab">Python2</a></li> <li><a href="#python3one" data-toggle="tab">Python3</a></li> <li><a href="#rubyone" data-toggle="tab">Ruby</a></li> <li><a href="#javaone" data-toggle="tab">Java</a></li> <li><a href="#rone" data-toggle="tab">R</a></li> <li><a href="#curlone" data-toggle="tab">Curl</a></li> <li><a href="#wgetone" data-toggle="tab">Wget</a></li> </ul> <div class='tab-content'> <div class='tab-pane active' id='exampleone'></div>  <script> var method = "GET"; var params = { url : "/vep/human/id/rs56116432?content-type=application/json", type : method, beforeSend : function () { $("#exampleone").append("<img src='/static/img/e-loader.gif'>"); return true; }, success : function (resp) { // If it has a documentElement we assume it is xml if (resp.documentElement == undefined) { if (typeof (resp) === "string") { $("#exampleone").append("<pre class=\"pre-scrollable\"> <code class=\"json\">" + resp + "</code></pre>"); $("#exampleone").each (function (i, block) { $("#exampleone>img").remove(); }) } else { var json = JSON.stringify(resp, undefined, 2); $("#exampleone").append("<pre class=\"pre-scrollable\"> <code class=\"json\">" + json + "</code></pre>") $("#exampleone").each (function (i, block) { hljs.highlightBlock(block); $("#exampleone>img").remove(); }) } } else { var xmlSerial = new XMLSerializer(); var xml_str = xmlSerial.serializeToString(resp); $("#exampleone").append("<pre id=\"preone\" class=\"pre-scrollable prettyprint\"></pre>"); $("#preone").text(xml_str); $("#exampleone").each (function (i, block) { hljs.highlightBlock(block); $("#exampleone>img").remove(); }) } }, error : function (resp, msg) { $("#exampleone").append("<pre id=\"preone\"></pre>"); $("#preone").text(resp.responseText); $("#exampleone>img").remove(); } }; if(method === "POST") { params.processData = false; params.data = ''; params.contentType = 'application/json'; params.accept = ''; } $.ajax( params); </script>   <div class='tab-pane' id='perlone'> <pre class="pre-scrollable prettyprint linenums"> use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://rest.ensembl.org'; my $ext = '/vep/human/id/rs56116432?'; my $response = $http->get($server.$ext, { headers => { 'Content-type' => 'application/json' } }); die "Failed!\n" unless $response->{success}; use JSON; use Data::Dumper; if(length $response->{content}) { my $hash = decode_json($response->{content}); local $Data::Dumper::Terse = 1; local $Data::Dumper::Indent = 1; print Dumper $hash; print "\n"; } </pre> </div>  <div class='tab-pane' id='python2one'> <pre class="pre-scrollable prettyprint linenums"> import requests, sys server = "https://rest.ensembl.org" ext = "/vep/human/id/rs56116432?" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print repr(decoded) </pre> </div>  <div class='tab-pane' id='python3one'> <pre class="pre-scrollable prettyprint linenums"> import requests, sys server = "https://rest.ensembl.org" ext = "/vep/human/id/rs56116432?" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print(repr(decoded)) </pre> </div>  <div class='tab-pane' id='rubyone'> <pre class="pre-scrollable prettyprint linenums"> require 'net/http' require 'uri' server='https://rest.ensembl.org' path = '/vep/human/id/rs56116432?' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'}) response = http.request(request) if response.code != "200" puts "Invalid response: #{response.code}" puts response.body exit end require 'rubygems' require 'json' require 'yaml' result = JSON.parse(response.body) puts YAML::dump(result) </pre> </div>  <div class='tab-pane' id='javaone'> <pre class="pre-scrollable prettyprint linenums"> import java.net.URL; import java.net.URLConnection; import java.net.HttpURLConnection; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.io.Reader; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://rest.ensembl.org"; String ext = "/vep/human/id/rs56116432?"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; httpConnection.setRequestProperty("Content-Type", "application/json"); InputStream response = connection.getInputStream(); int responseCode = httpConnection.getResponseCode(); if(responseCode != 200) { throw new RuntimeException("Response code was not 200. Detected response was "+responseCode); } String output; Reader reader = null; try { reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); StringBuilder builder = new StringBuilder(); char[] buffer = new char[8192]; int read; while ((read = reader.read(buffer, 0, buffer.length)) > 0) { builder.append(buffer, 0, read); } output = builder.toString(); } finally { if (reader != null) try { reader.close(); } catch (IOException logOrIgnore) { logOrIgnore.printStackTrace(); } } System.out.println(output); } } </pre> </div>  <div class='tab-pane' id='rone'> <pre class="pre-scrollable prettyprint linenums"> library(httr) library(jsonlite) library(xml2) server <- "https://rest.ensembl.org" ext <- "/vep/human/id/rs56116432?" r <- GET(paste(server, ext, sep = ""), content_type("application/json")) stop_for_status(r) # use this if you get a simple nested list back, otherwise inspect its structure # head(data.frame(t(sapply(content(r),c)))) head(fromJSON(toJSON(content(r)))) </pre> </div>  <div class='tab-pane' id='curlone'> <pre class="pre-scrollable prettyprint linenums"> curl 'https://rest.ensembl.org/vep/human/id/rs56116432?' -H 'Content-type:application/json' </pre> </div>  <div class='tab-pane' id='wgetone'> <pre class="pre-scrollable prettyprint linenums"> wget -q --header='Content-type:application/json' 'https://rest.ensembl.org/vep/human/id/rs56116432?' -O - </pre> </div> </div>  </div> <div class="span2"> <h3>Resource Information</h3> <table class="table table-condensed table-striped"> <tbody> <tr><td>Methods</td><td>GET</td></tr> <tr><td>Response formats</td><td>json<br>xml<br>jsonp</td></tr> </tbody> </table> </div> </div> </div> <footer class="footer"> <div class="container"> <p class="pull-right"><a href="#">Back to top</a></p> <p>Ensembl REST API (Version 15.8) © Nov 2024 <a href='http://www.ebi.ac.uk'>EBI</a></p> </div> </footer> <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script> <script src='/_asset/fe9f7c398905c6888db2ca28ab1bef94.js'></script> </body> </html>

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Ensembl Rest API - GET vep/:species/id/:id