GET vep/:species/id/:id

Fetch variant consequences based on a variant identifier

Parameters

Required

NameTypeDescriptionDefaultExample Values
id String Query ID. Supports dbSNP, COSMIC and HGMD identifiers - ENSVATH12367453
ENSVATH00550254
species String Species name/alias - arabidopsis_thaliana
Arabidopsis thaliana

Optional

NameTypeDescriptionDefaultExample Values
Blosum62 Boolean Include BLOSUM62 amino acid conservation score (plugin details) 0 -
CSN Boolean Reports Clinical Sequencing Nomenclature (CSN) for variants (plugin details) 0 -
Conservation Boolean Retrieves a conservation score from the Ensembl Compara databases for variant positions (plugin details) 0 -
ExAC Boolean Reports allele frequencies from the Exome Aggregation Consortium (plugin details) 0 -
GeneSplicer Boolean Detects splice sites in genomic DNA (plugin details) 0 -
MaxEntScan Boolean Sequence motif and maximum entropy based splice site consensus predictions (plugin details) 0 -
UpDownDistance Integer Change the distance to transcript for which VEP assigns upstream and downstream consequences (plugin details) 5000 -
callback String Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. - randomlygeneratedname
canonical Boolean Include a flag indicating the canonical transcript for a gene 0 -
ccds Boolean Include CCDS transcript identifiers 0 -
dbNSFP String Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See dbNSFP README for field list. (plugin details) Not used LRT_pred,MutationTaster_pred
dbscSNV Boolean Predictions for splicing variants from dbscSNV. (plugin details) 0 -
domains Boolean Include names of overlapping protein domains 0 -
hgvs Boolean Include HGVS nomenclature based on Ensembl stable identifiers 0 -
miRNA Boolean Determines where in the secondary structure of a miRNA a variant falls (plugin details) 0 -
numbers Boolean Include affected exon and intron positions within the transcript 0 -
protein Boolean Include Ensembl protein identifiers 0 -
xref_refseq Boolean 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 0 -

Example Requests

/vep/Arabidopsis thaliana/id/ENSVATH00550254?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'http://rest.ensemblgenomes.org';
my $ext = '/vep/Arabidopsis%20thaliana/id/ENSVATH00550254?';
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";
}

import requests, sys

server = "http://rest.ensemblgenomes.org"
ext = "/vep/Arabidopsis thaliana/id/ENSVATH00550254?"

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)

import requests, sys

server = "http://rest.ensemblgenomes.org"
ext = "/vep/Arabidopsis thaliana/id/ENSVATH00550254?"

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))

require 'net/http'
require 'uri'

server='http://rest.ensemblgenomes.org'
path = '/vep/Arabidopsis%20thaliana/id/ENSVATH00550254?'

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)

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 = "http://rest.ensemblgenomes.org";
    String ext = "/vep/Arabidopsis%20thaliana/id/ENSVATH00550254?";
    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);
  }
}


curl 'http://rest.ensemblgenomes.org/vep/Arabidopsis%20thaliana/id/ENSVATH00550254?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://rest.ensemblgenomes.org/vep/Arabidopsis thaliana/id/ENSVATH00550254?'  -O -

/vep/Arabidopsis thaliana/id/ENSVATH12367453?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'http://rest.ensemblgenomes.org';
my $ext = '/vep/Arabidopsis%20thaliana/id/ENSVATH12367453?';
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";
}

import requests, sys

server = "http://rest.ensemblgenomes.org"
ext = "/vep/Arabidopsis thaliana/id/ENSVATH12367453?"

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)

import requests, sys

server = "http://rest.ensemblgenomes.org"
ext = "/vep/Arabidopsis thaliana/id/ENSVATH12367453?"

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))

require 'net/http'
require 'uri'

server='http://rest.ensemblgenomes.org'
path = '/vep/Arabidopsis%20thaliana/id/ENSVATH12367453?'

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)

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 = "http://rest.ensemblgenomes.org";
    String ext = "/vep/Arabidopsis%20thaliana/id/ENSVATH12367453?";
    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);
  }
}


curl 'http://rest.ensemblgenomes.org/vep/Arabidopsis%20thaliana/id/ENSVATH12367453?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://rest.ensemblgenomes.org/vep/Arabidopsis thaliana/id/ENSVATH12367453?'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
jsonp