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href="/info/docs/tools/" title="Ensembl Tools">Ensembl Tools</a></li><li><a href="/info/docs/tools/vep/" title="Ensembl Variant Effect Predictor (VEP)">Ensembl Variant Effect Predictor (VEP)</a></li><li><a href="/info/docs/tools/vep/script/" title="VEP command line">VEP command line</a></li><li class="last">Download and install</li></ul> <div id="content"><div id="static"> <style> tr:nth-child(odd) {background-color: #f0f0f0;} code {background-color: rgb(240, 240, 240); font-family: Courier New, Courier, monospace;} </style> <div> <div style="float:right"><img src="/img/vep_logo.png"/></div> <h1 id="top"><span style="color:#006;padding-right:15px">Variant Effect Predictor</span><span style="color:#666"><img src="/i/16/download.png"> Download and install</span></h1> <hr/> <div> <div style="float:left" class="info "> <h3 id="container">Note</h3> <div class="message-pad"> <p>To address potential installation challenges with VEP dependencies on newer systems, we recommend using <a href="#docker">Docker</a> or <a href="#singularity">Singularity</a> containers. <p>These containerised environments enable to access all the latest VEP features without the hassle of installing dependencies directly on your system. Additionally, they are highly compatible with computer clusters.</p> </div> </div> <div class="clear"></div> </div> <h2 id="download">Download</h2> <p>Download ensembl-vep package (see below the different ways to download it) and then follow the <a href="#installer">installation instructions</a>.</p> <br /> <h3>Using Git</h3> <h4><img src="/i/bullet_1.gif" style="vertical-align:baseline"/> Clone the Git repository</h4> <p> Use git to download the ensembl-vep package:</p> <pre class="code sh_sh">git clone https://github.com/Ensembl/ensembl-vep.git cd ensembl-vep</pre> <br /> <h4><img src="/i/bullet_1.gif" style="vertical-align:baseline"/> Update to a newer version</h4> <p>To update from a previous version: </p> <pre class="code sh_sh">cd ensembl-vep git pull git checkout release/113 perl INSTALL.pl</pre> <br /> <h4><img src="/i/bullet_1.gif" style="vertical-align:baseline"/> Use an older version</h4> <p> To use an older version (this example shows how to set up release 87): </p> <pre class="code sh_sh">cd ensembl-vep git checkout release/87 perl INSTALL.pl</pre> <br /> <h3>Download the Zipped package file</h3> <p> Users without the git utility installed may download a zip file from GitHub, though we would always recommend using git if possible.</p> <pre class="code sh_sh" id="nogit">curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/113.zip unzip 113.zip cd ensembl-vep-release-113/</pre> <br /> <h3 id="toolsversions"> Previous versions (ensembl-tools)</h3> <p> Previously VEP was available as part of the ensembl-tools package (see the <a href="http://e87.ensembl.org/info/docs/tools/vep/script/index.html">Ensembl archive site</a> for documentation). The following downloads are available for archival purposes. <a class="button" href="#toolsversions" onclick="show_hide('toolsversions');" id="a_toolsversions">Show versions</a> </p> <div id="div_toolsversions" style="display:none;"> <ul> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/87.zip">Download version 87</a> (Ensembl 87) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/86.zip">Download version 86</a> (Ensembl 86) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/85.zip">Download version 85</a> (Ensembl 85) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/84.zip">Download version 84</a> (Ensembl 84) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/83.zip">Download version 83</a> (Ensembl 83) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/82.zip">Download version 82</a> (Ensembl 82) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/81.zip">Download version 81</a> (Ensembl 81) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/80.zip">Download version 80</a> (Ensembl 80) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/79.zip">Download version 79</a> (Ensembl 79) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/78.zip">Download version 78</a> (Ensembl 78) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/77.zip">Download version 77</a> (Ensembl 77) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/76.zip">Download version 76</a> (Ensembl 76) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/75.zip">Download version 75</a> (Ensembl 75) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/74.zip">Download version 74</a> (Ensembl 74) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/73.zip">Download version 73</a> (Ensembl 73) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/72.zip">Download version 72</a> (Ensembl 72) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/71.zip">Download version 71</a> (Ensembl 71) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/70.zip">Download version 2.8</a> (Ensembl 70) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/69.zip">Download version 2.7</a> (Ensembl 69) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/68.zip">Download version 2.6</a> (Ensembl 68) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/67.zip">Download version 2.5</a> (Ensembl 67) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/66.zip">Download version 2.4</a> (Ensembl 66) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/65.zip">Download version 2.3</a> (Ensembl 65) </li> <li><a href="https://github.com/Ensembl/ensembl-tools/archive/release/64.zip">Download version 2.2</a> (Ensembl 64 - ensembl-tools/scripts/variant_effect_predictor) </li> <li><a href="https://github.com/Ensembl/ensembl-variation/archive/release/63.zip">Download version 2.1</a> (Ensembl 63) </li> <li><a href="https://github.com/Ensembl/ensembl-variation/archive/release/62.zip">Download version 2.0</a> (Ensembl 62 - ensembl-variation/scripts/examples) </li> </ul> </div><hr/> <h2 id="new">What's new?</h2> <div class="toolbox" style="float:none;padding:6px"> <h4>New in version 113 <i>(October 2024)</i></h4> <ul> <li>gnomAD frequency data updated to v4.1 for both genomes and exomes.</li> <li>Support for GENCODE primary transcript set added. See, <a href="vep_options.html#opt_gencode_primary">--gencode_primary</a> and <a href="vep_options.html#opt_flag_gencode_primary">--flag_gencode_primary</a>.</li> <li>Support added for <a href="vep_options.html#opt_mane">--mane</a>, <a href="vep_options.html#opt_mane_select">--mane_select</a>, and <a href="vep_options.html#opt_canonical">--canonical</a> when GFF/GTF file used as annotation source.</li> <li>Nextflow VEP now suppots other input data formats besides VCF. For supported formats see - <a href="../vep_formats.html#input">Data formats</a>.</li> <li>Plugin support added to REST and Web for: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/RiboseqORFs.pm" rel="external">RiboseqORFs</a></li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/REVEL.pm" rel="external">REVEL</a></li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/ClinPred.pm" rel="external">ClinPred</a></li> </ul> <li>Plugin support added to Web for: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Paralogues.pm" rel="external">Paralogues</a></li> </ul> <li>Plugin support added to REST for: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/LOEUF.pm" rel="external">LOEUF</a></li> </ul> <li>Plugin data version updated for CADD (v1.6 to v1.7) and dbNSFP (4.5c to 4.7c).</li> </ul> </div> <br /> <h4 id="history">Previous version history - from version 88: <a class="button" href="#history" onclick="show_hide('history');" id="a_history" style="font-weight:normal">Show</a></h4> <div id="div_history" style="display:none"> <h4>New in version 112 <i>(May 2024)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Enhanced Structural Variant Support:</li> <ul> <li>Added support for CNV:TR</li> <li>Enabled the use of chromosome synonyms in breakends</li> <li>Report consequences for each breakend and enable the input of single breakends</li> </ul> <li>New plugins (supported on CLI, Web and REST): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/AlphaMissense.pm" rel="external">AlphaMissense</a> - annotates missense variants with the pre-computed AlphaMissense pathogenicity scores. AlphaMissense is a deep learning model developed by Google DeepMind that predicts the pathogenicity of single nucleotide missense variants. </li> </ul> <li>New plugins (supported on CLI and Web): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/RiboseqORFs.pm" rel="external">RiboseqORFs</a> - uses a standardized catalog of human Ribo-seq ORFs to re-calculate consequences for variants located in these translated regions</li> </ul> <li>New plugins (supported on CLI): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Paralogues.pm" rel="external">Paralogues</a> - fetches variants overlapping the genomic coordinates of amino acids aligned between paralogue proteins</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/AVADA.pm" rel="external">AVADA</a> - Automatic VAriant evidence DAtabase is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/GeneBe.pm" rel="external">GeneBe</a> - A plugin kindly contributed by the GeneBe team, it retrieves automatic ACMG variant classification data from https://genebe.net/</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/PhenotypeOrthologous.pm" rel="external">PhenotypeOrthologous</a> A VEP plugin that retrieves phenotype information associated with orthologous genes from model organisms</li> </ul> <li>Plugin support added to REST and Web for: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/CADD.pm" rel="external">CADD_SV</a></li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/CADD.pm" rel="external">CADD</a> scores for <i>Sus scrofa</i></li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/DosageSensitivity.pm" rel="external">Dosage Sensitivity</a></li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Enformer.pm" rel="external">Enformer</a></li> </ul> </ul> </div> <h4>New in version 111 <i>(January 2024)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New option <a href="vep_options.html#opt_individual_zyg">--individual_zyg</a> returns a single list of individuals and their zygosity (instead of a separate line of output for each individual and variant combination like in <a href="vep_options.html#opt_individual">--individual</a>)</li> <li><a href="vep_custom.html">Custom annotation</a> has been improved with the following options:</li> <ul> <li><a href="vep_custom.html#opt_num_records">num_records</a> to limit the number of matching records (50 by default)</li> <li><a href="vep_custom.html#opt_summary_stats">summary_stats</a> to calculate summary statistics (min, mean, max, count, sum) using annotation scores (not used by default)</li> </ul> <li>New plugin (supported on CLI, REST and web): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/OpenTargets.pm" rel="external">OpenTargets</a> - adds locus-to-gene (L2G) scores to predict causal genes at GWAS loci from Open Targets Genetics</li> </ul> <li>New plugin (supported on CLI and REST): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Enformer.pm" rel="external">Enformer</a> - adds pre-calculated predictions of variant impact on gene expression</li> </ul> <li>New plugins (supported on CLI): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/BayesDel.pm" rel="external">BayesDel</a> - adds a deleteriousness meta-score combining multiple deleteriousness predictors</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/DeNovo.pm" rel="external">DeNovo</a> - identifies de novo variants in a VCF file. This plugin requires a pedigree (.ped) file</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/SpliceVault.pm" rel="external">SpliceVault</a> - predicts exon-skipping events and activated cryptic splice sites based on the most common mis-splicing events around a splice site</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/DosageSensitivity.pm" rel="external">DosageSensitivity</a> - annotates the likelihood of a gene being haploinsufficient or triplosensitive</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/VARITY.pm" rel="external">VARITY</a> - adds pre-calculated pathogenicity scores of rare human missense variants</li> </ul> </ul> </div> <h4>New in version 110 <i>(July 2023)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New plugins (supported on CLI): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/TranscriptAnnotator.pm" rel="external">TranscriptAnnotator</a> - a VEP plugin that annotates variant-transcript pairs</li> </ul> <li>New Plugins (supported on CLI, REST and web): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Geno2MP.pm" rel="external">Geno2MP</a> - adds information from Geno2MP, a web-accessible database of rare variant genotypes linked to phenotypic information</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/MaveDB.pm" rel="external">MaveDB</a> - adds information from MaveDB, a database that holds experimentally determined measures of variant effect</li> </ul> </ul> </div> <h4>New in version 109 <i>(February 2023)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li><a href="https://hub.docker.com/r/ensemblorg/ensembl-vep">VEP Docker image</a> now includes all VEP plugins</li> <li>New plugin (supported on CLI): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/GWAS.pm" rel="external">GWAS</a> - reports genome-wide association study data from GWAS catalog</li> </ul> <li>Plugins now available in REST and web: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/UTRAnnotator.pm" rel="external">UTRAnnotator</a> - annotates the effect of 5' UTR variant especially for variant creating/disrupting upstream ORFs</li> </ul> <li>Plugins now available in REST: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/NMD.pm" rel="external">NMD</a> - predicts if a variant allows transcript to escape nonsense-mediated mRNA decay based on certain rules</li> </ul> <li>Plugin LOEUF replaces Loftool in the web with more recent ‘loss-of-function’ score for variants</li> <li>Deprecated Plugins: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/miRNA.pm" rel="external">miRNA</a> - this plugin was fully deprecated in favour of --mirna flag (in web and REST)</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/ExAC.pm" rel="external">ExAC</a> - this plugin was deprecated given that VEP cache includes ExAC data as part of gnomAD</li> </ul> <li>SIFT version has been updated from 5.2.2 to 6.2.1 (except for human GRCh37)</li> <li>PolyPhen-2 version has been updated from 2.2.2 to 2.2.3 (except for human GRCh37)</li> </ul> </div> <h4>New in version 108 <i>(October 2022)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New plugin (supported on CLI, REST, and web): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/mutfunc.pm" rel="external">mutfunc</a> - predicts destabilization of protein structure, interaction and others features by a variant (GRCh38 only)</li> </ul> <li>Plugin feature extension: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/IntAct.pm" rel="external">IntAct</a> - 4 new species are now supported - rat, chicken (red jungle fowl), yeast, and arabidopsis</li> </ul> </ul> </div> <h4>New in version 107 <i>(July 2022)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New plugin (supported on CLI, REST, and web): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/EVE.pm" rel="external">EVE</a> - annotates human variants using EVA classification method based solely on evolutionary sequences (GRCh38 only)</li> </ul> <li>Plugins now available in REST and web (already available in CLI): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/GO.pm" rel="external">GO</a> - retrieves Gene Ontology terms associated with transcripts/translations</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/IntAct.pm" rel="external">IntAct</a> - annotates human variants which fall in interaction sites, as described in the IntAct database</li> </ul> <li>Plugins now available in web (already available in CLI): </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/NMD.pm" rel="external">NMD</a> - predicts if a stop_gained variant allows transcript to escape nonsense-mediated mRNA decay based on certain rules</li> </ul> <li>Readthrough transcripts are now removed from cache</li> <li>Transcripts of biotype ‘artifact’ which are artifactual duplication are now removed from cache and not accessible using database</li> <li>gnomaAD allele frequencies are now available for exomes and genomes separately through —af_gnomade and —af_gnomadg options respectively. The —af_gnomad option have same function as --af_gnomade.</li> </ul> </div> <h4>New in version 106 <i>(April 2022)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New plugins for command line use: </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/IntAct.pm" rel="external">IntAct</a> - annotates human variants which fall in interaction sites, as described in the IntAct database</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/CAPICE.pm" rel="external">CAPICE</a> - integrates scored from a machine-learning-based method for prioritizing pathogenic variants (GRCh37 only)</li> </ul> <li>Nextflow pipeline:</li> <ul> <li>A new configurable pipeline is available to run Ensembl VEP efficiently on large scale VCF</li> </ul> </ul> </div> <h4>New in version 105 <i>(December 2021)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>3 new Sequence Ontology terms are reported for more detailed splice consequence annotation </li> <ul> <li>splice_donor_5th_base_variant (<a rel="external" href="http://www.sequenceontology.org/miso/current_release/term/SO:0001787">SO:0001787</a>)</li> <li>splice_donor_region_variant (<a rel="external" href="http://www.sequenceontology.org/miso/current_release/term/SO:0002170">SO:0002170</a>)</li> <li>splice_polypyrimidine_tract_variant (<a rel="external" href="http://www.sequenceontology.org/miso/current_release/term/SO:0002169">SO:0002169</a>)</li> </ul> <li>New plugins </li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/ClinPred.pm" rel="external">ClinPred</a> - adds pre-calculated scores from ClinPred which helps identify disease-relevant missense variants</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/NMD.pm" rel="external">NMD</a> - predicts whether a stop-gained variant will allow a transcript to escape nonsense-mediated decay</li> </ul> <li>Condel scores are no longer available via the VEP web interface as they have not been updated since 2014 and newer scores like CADD and REVEL are available</li> </ul> </div> <h4>New in version 104 <i>(May 2021)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Human GRCh37 cache files now include dbSNP 154! </li> <li><a href="vep_options.html#opt_var_synonyms">--var_synonyms</a> output structure has been altered when used with <a href="vep_options.html#opt_json">--json</a></li> </ul> <ul><li>VEP Plugins:</li> <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/dbNSFP.pm" rel="external">dbNSFP</a> - now supports matching by peptides</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/SpliceAI.pm" rel="external">SpliceAI</a> - now compares gene symbols to improve score accuracy</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/DisGeNET.pm" rel="external">DisGeNET</a> - improvements have been made to output structure</li> </ul> </ul> </div> <h4>New in version 103 <i>(February 2021)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li><b>New:</b> Variant Recoder is now available as a web tool</li> <li>Variant Recoder output is now allele specific</li> </ul> <ul><li>Web VEP Options:</li> <ul> <li>Variant Synonyms are now available through the web interface</li> <li>MasterMind results are available through the REST and web interfaces</li> </ul> </ul> <ul><li>VEP Options:</li> <ul> <li><a href="vep_options.html#opt_mane">--mane</a> : Now provides additional MANE Plus Clinical annotations alongside MANE Select</li> <li><a href="vep_options.html#opt_mane_select">--mane_select</a> : Returns MANE Select annotations </li> </ul> </ul> </div> <h4>New in version 102 <i>(November 2020)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>VEP options: <ul> <li><a href="vep_options.html#opt_uniprot">--uniprot</a>: Now we report precise Ensembl translation to UniProt isoform mappings.</li> <li><a href="vep_options.html#opt_spdi">--spdi</a> - <b>new</b>: Add genomic <a rel="external" href="https://www.ncbi.nlm.nih.gov/variation/notation/", target="_blank">SPDI</a> notation.</li> </ul> </li> <li> Web VEP options: <ul> <li>Shifting variants in the 3' direction with <a href="vep_options.html#opt_shift_3prime">--shift_3prime</a> and <a href="vep_options.html#opt_shift_genomic">--shift_genomic</a> is now supported through the web interface.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/DisGeNET.pm" rel="external">DisGeNET</a> - <b>new</b>: DisGeNET results are available through the web interface.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/SpliceAI.pm" rel="external">SpliceAI</a> - <b>new</b>: SpliceAI pre-calculated scores are available through the web interface.</li> </ul> </li> <li> VEP filter options: <ul> <li><a href="vep_filter.html#opt_softfilter">--soft_filter</a> - <b>new</b>: Option to only flag the failing variation in the FILTER column and keep the entries in the output VCF file.</li> </ul> </li> </ul> </div> <br/> <h4>New in version version 101 <i>(August 2020)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New options: <ul> <li><a href="vep_options.html#opt_var_synonyms">--var_synonyms</a>: Report known synonyms for colocated variants. Must be used with <a href="vep_options.html#opt_cache">--cache</a>.</li> </ul> </li> <li>VEP plugins: <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/neXtProt.pm" rel="external">neXtProt</a> - <b>new</b>: neXtProt retrieves comprehensive human-centric protein-related data for missense variants </li> </ul> </li> </ul> </div> <br/> <h4>New in version 100 <i>(April 2020)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Human GRCh37 variant and phenotype data has been updated with multiple data sets including dbSNP153, ClinVar’s 201912 release and COSMIC release 90</li> <li>The GRCh37 RefSeq transcript set has been updated to NCBI's 1st November 2019 release (initially annotated on GCF_000001405.25)! <li>New options: <ul> <li><a href="vep_options.html#opt_shift_3prime">--shift_3prime</a>: Right aligns all variants relative to their associated transcripts prior to consequence calculation</li> <li><a href="vep_options.html#opt_shift_genomic">--shift_genomic</a>: Right aligns all variants, including intergenic variants, before consequence calculation and updates the <i>Location</i> field</li> </ul> </li> <li>VEP plugins: <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/SpliceAI.pm" rel="external">SpliceAI</a> - <b>new</b>: SpliceAI is a deep neural network, developed by Illumina, Inc that predicts splice junctions from an arbitrary pre-mRNA transcript sequence.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/DisGeNET.pm" rel="external">DisGeNET</a> - <b>new</b>: DisGeNET is a database containing human variant-disease associations</li> </ul> </li> </ul> </div> <br/> <h4>New in version 99 <i>(January 2020)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Human GRCh38 cache files now contain variants from dbSNP153</li> <li>New options have been added to REST: <ul> <li>vcf_string: VEP can now provide a VCF-like string representing the input variant </li> <li>transcript_version: Add version numbers to Ensembl transcript identifiers </li> <li>SpliceRegion: Provides granular predictions of splicing effects (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/SpliceRegion.pm">Details</a>) </li> <li>LoF: LOFTEE implements a set of filters to predict LoF (loss-of-function) variants. (<a target="_blank" href="https://github.com/konradjk/loftee/blob/master/README.md">Details</a>) </li> </ul> </li> </ul> </div> <br/> <h4>New in version 98 <i>(September 2019)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Human GRCh38 cache files now contain variants from dbSNP152</li> <li>This employs a new clustering strategy which may result in different rsIDs being reported as known variants for some insertions and deletions - for more information see <a href='http://www.ensembl.info/2019/08/29/coming-soon-to-an-ensembl-near-you-dbsnp-2-0/'> here </a></li> <li><a href="vep_options.html#opt_clin_sig_allele">--clin_sig_allele</a> has been updated to be used by default</li> <li>New options: <ul> <li><a href="vep_options.html#opt_custom_multi_allelic">--custom_multi_allelic</a>: prevents VEP from assuming that comma separated lists in custom annotations are allele specific</li> </ul> </li> <li>MANE attributes are now included within VEP cache files, web VEP and REST</li> <li>VEP plugins: <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/satMutMPRA.pm" rel="external">satMutMPRA</a> - <b>new</b>: measures variant effects on gene RNA expression for 21 regulatory elements</li> </ul> </li> <li> VEP Installer: </li> <ul> <li>HTSLib v1.9 is now installed by default (previously v1.3.2)</li> <li>Bio::DB::HTS v2.11 is now installed by default (previously v2.9)</li> <li>New option 'PLUGINSDIR' allows you to specify the installation directory for plugins</li> </ul> </ul> </div> <br/> <h4>New in version 97 <i>(July 2019)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Allele-specific clinical significance reported (it was previously variant-specific).</li> <li>New options: <ul> <li><a href="vep_options.html#opt_clin_sig_allele">--clin_sig_allele</a>: report allele specific clinical significance.</li> <li><a href="vep_options.html#opt_mane">--mane</a>: report if a transcript is the MANE Select.</li> <li><a href="vep_options.html#opt_max_sv_size">--max_sv_size</a>: extend the maximum Structural Variant size VEP can process.</li> <li><a href="vep_options.html#opt_no_check_variants_order">--no_check_variants_order</a>: permit the use of unsorted input files (WARNING - this is slow and requires more memory).</li> <li><a href="vep_options.html#opt_overlaps">--overlaps</a>: report the proportion and length of a transcript overlapped by a structural variant in VCF format.</li> </ul> </li> <li>Include the <a href="vep_options.html#opt_mane">--mane</a> option into the <a href="vep_options.html#opt_everything">--everything</a> group option.</li> <li>Update <a href="vep_options.html#opt_pick">--pick</a> and <a href="vep_options.html#opt_pick_order">--pick_order</a> to support MANE Select transcripts.</li> <li>Check if the input variants are ordered: non ordered variants slow down VEP and require more memory.</li> <li>Skip annotation of complex and long structural variants and display a warning message.</li> <li>Variant recoder: add an option <a href="/info/docs/tools/vep/recoder/index.html#opt_vcf_string">--vcf_string</a> to return results in VCF format.</li> <li>VEP plugins: <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/FunMotifs.pm" rel="external">FunMotifs</a> - <b>new</b>: provide information about overlapping tissue-specific transcription factor motifs.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Mastermind.pm" rel="external">Mastermind</a> - <b>new</b>: reports variants that have clinical evidence cited in the medical literature.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/StructuralVariantOverlap.pm" rel="external">StructuralVariantOverlap</a> - <b>new</b>: provide information from overlapping structural variants.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/G2P.pm" rel="external">G2P</a> - <b>update</b>: now the plugin can be run offline.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Phenotypes.pm" rel="external">Phenotypes</a> - <b>update</b>: change the format of the data file (from BED to GVF).</li> </ul> </li> <li>VEP web tool: the transcript identifiers are now returned with versions unless otherwise specified.</li> <li>VEP installer: tabix-indexed variant cache files are now installed by default.</li> </ul> </div> <br /> <h4>New in version 96 <i>(April 2019)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Add <b>SPDI</b> format for VEP (input) and Variant Recoder (input and output).</li> <li>Update VEP cache with <b>gnomAD 2.1</b> (human).</li> <li>Update the Docker VEP base image to <b>Ubuntu 18.04</b>.</li> <li>Retire deprecated flags: --gmaf, --maf_1kg, --maf_esp, --maf_exac, --check_alleles, --html, --gvf.</li> <li>Retire legacy code about the pileup input format, which is no longer supported. <li>Deprecate the installation flag "--VERSION"</li> <li>Force numbers to be encoded as numbers in JSON output</li> <li>VEP plugins: <ul> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/NearestExonJB.pm" rel="external">NearestExonJB</a> - <b>new</b>: find the nearest exon junction boundary to a coding sequence variant.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Conservation.pm" rel="external">Conservation</a> - update: can use BigWig files instead of the Ensembl Compara database.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/dbNSFP.pm" rel="external">dbNSFP</a> - update: support of the dbNSFP data version 4.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/Phenotypes.pm" rel="external">Phenotypes</a> - update: possibility to report the phenotype description(s) and other information.</li> <li><a href="//github.com/Ensembl/VEP_plugins/blob/release/113/PostGAP.pm" rel="external">PostGAP</a> - update: replace the plugin name POSTGAP to PostGAP.</li> </ul> </li> </ul> </div> <br /> <h4>New in version 95 <i>(January 2019)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>The VEP parser is now more permissive for the GFF files (ID attribute only required for genes and transcripts)</li> <li>Add new option <a href="vep_options.html#opt_show_ref_allele">--show_ref_allele</a> to include the allele reference in the VEP default output and the tab output formats</li> <li>Add a warning message when the VEP annotations INFO field hasn't been found/recognised in the VCF input file</li> <li>VEP Docker image: <ul> <li>Reduce the size of the VEP Docker image by about 45%.</li> <li>Include the Linkage disequilibrium script in the VEP Docker image, making possible to run the LD plugin</li> </ul> </li> <li>New VEP plugins: <ul> <li> <a href="//github.com/Ensembl/VEP_plugins/blob/release/113/ReferenceQuality.pm" rel="external">Reference quality</a> </li> <li> <a href="//github.com/Ensembl/VEP_plugins/blob/release/113/POSTGAP.pm" rel="external">OpenTargets results (POSTGAP)</a> </li> <li> <a href="//github.com/Ensembl/VEP_plugins/blob/release/113/SingleLetterAA.pm" rel="external">Single letter amino acid for HGVS</a> </li> </ul> </li> </ul> </div> <br /> <h4>New in version 94 <i>(October 2018)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>RefSeq transcript version updated.</li> <li>Minor updates on the <a href="/Tools/VEP">VEP web tool</a> interface.</li> <li>When the input data format is not specified on the command line, VEP attempts to detect it. The assumed format is now reported in verbose mode (<a href="vep_options.html#opt_verbose">--verbose</a>).</li> <li>VEP assigns assigned the consequence types <i>TF_binding_site_variant</i>, <i>TFBS_ablation</i>, <i>TFBS_fusion</i>, <i>TFBS_amplification</i> and <i>TFBS_translocation</i> to human and mouse variants which overlapped motif features. These annotations will not be available in VEP caches for human in release 94 so must be added as a <a href="/info/docs/tools/vep/script/vep_custom.html">custom annotation</a>.</li> </ul> </div> <br /> <h4>New in version 93 <i>(July 2018)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>Update the JSON output format (allele frequencies) for the <a href="//rest.ensembl.org/#VEP" rel="external">Ensembl REST - VEP</a> endpoints. <a href="//github.com/Ensembl/ensembl-rest/wiki/Change-log#70---2018-06" rel="external">See more information</a>.</li> <li>The new Ensembl release brings more frequency data from <a href="http://gnomad.broadinstitute.org/" rel="external">gnomAD</a>.</li> <li>Add the possibility to print the content of the FILTER column (from the VCF custom annotation files) in the output.</li> <li>Include the <a href="//github.com/Ensembl/ensembl-xs" rel="external">Ensembl/ensembl-xs</a> repository in Docker image to speed up the VEP container.</li> <li>Add a new consequence 'extended_intronic_splice_region_variant' in the <a href="//github.com/Ensembl/VEP_plugins/blob/release/113/SpliceRegion.pm" rel="external">SpliceRegion</a> VEP plugin.</li> </ul> </div> <br /> <h4>New in version 92 <i>(April 2018)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New VEP plugin <a href="//www.ncbi.nlm.nih.gov/pubmed/27666373" rel="external">REVEL</a> (see <a href="//github.com/Ensembl/VEP_plugins/blob/release/92/REVEL.pm" rel="external">REVEL plugin</a>).</li> <li>Get ambiguity code with <a href="vep_options.html#opt_ambiguity">--ambiguity</a>.</li> <li><a href="vep_cache.html#gff">GFF/GTF files</a> with exons assigned to multiple transcripts are now supported.</li> <li>Improved 1000 Genomes Project frequencies.</li> </ul> </div> <br /> <h4>New in version 91 <i>(December 2017)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>New input format "<a href="../vep_formats.html#region">region</a>" allows REST-style input to VEP.</li> <li>Replace your input variant reference allele with the correct one from the genome with <a href="vep_options.html#opt_lookup_ref">--lookup_ref</a>.</li> <li>Add version numbers to Ensembl transcripts with <a href="vep_options.html#opt_transcript_version">--transcript_version</a>.</li> </ul> </div> <br /> <h4>New in version 90 <i>(August 2017)</i></h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li><a href="http://gnomad.broadinstitute.org/" rel="external">gnomAD</a> exomes allele frequencies now available with <a href="vep_options.html#opt_af_gnomade">--af_gnomad</a>, replacing ExAC. gnomAD genomes and ExAC are <a href="vep_example.html#gnomad">available via custom annotation</a>.</li> <li>VEP is now available as a <a href="#docker">Docker image</a>.</li> <li>RefSeq transcripts in VEP cache files are now <a href="vep_other.html#refseq">"corrected" from the reference genome sequence</a>.</li> <li>VEP's algorithm for matching colocated known variants has been overhauled - <a href="vep_other.html#colocated">details</a>.</li> <li>Change VEP's default (5kb) up/downstream distance with <a href="vep_options.html#opt_distance">--distance</a>. This supercedes the functionality of the UpDownDistance VEP plugin.</li> <li>Feed input directly to VEP with <a href="vep_options.html#opt_input_data">--input_data</a>.</li> <li>Suppress header output with <a href="vep_options.html#opt_no_headers">--no_headers</a>.</li> <li>Detailed <a href="#bigfile">installation instructions for Bio::DB::BigFile</a> to access bigWig custom annotation files.</li> </ul> </div> <br /> <h4> New in version 89 <i>(May 2017)</i> </h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>exclude known variants with unknown (null) alleles with <a href="vep_options.html#opt_exclude_null_alleles">--exclude_null_alleles</a>.</li> <li>write compressed output with <a href="vep_options.html#opt_compress_output">--compress_output</a>.</li> <li>improved matching of alleles in <a href="vep_custom.html">custom VCF files</a>.</li> <li>API perldoc documentation added.</li> </ul> </div> <br /> <h4> New in version 88 <i>(March 2017)</i> </h4> <div class="left-margin" style="border-left:2px solid #7b8baf"> <ul> <li>ensembl-vep is now the officially supported version of VEP</li> <li>Documentation updated to reflect switch to ensembl-vep. See the <a href="http://e87.ensembl.org/info/docs/tools/vep/script/index.html">Ensembl archive site</a> for documentation of the obsolete ensembl-tools VEP.</li> <li>The VEP script is now named simply <code>vep</code> (formerly <code>variant_effect_predictor.pl</code> or <code>vep.pl</code>)</li> <li>Directly use tabix-indexed <a href="vep_cache.html#gff">GFF/GTF files as annotation sources</a></li> <li>Allele-specific reporting of frequencies (<a href="vep_options.html#opt_af">--af</a> and more) and <a href="vep_custom.html">custom VCF annotations</a></li> <li><a href="vep_options.html#opt_check_existing">--check_existing</a> now compares alleles by default, disable with <a href="vep_options.html">--no_check_alleles</a></li> <li>Report the highest allele frequency observed in any population from 1000 genomes, ESP or ExAC using <a href="vep_options.html#opt_max_af">--max_af</a></li> <li>Get genomic HGVS nomenclature with <a href="vep_options.html#opt_hgvsg">--hgvsg</a></li> <li>Find the gene or transcript with the nearest transcription start site (TSS) to each input variant with <a href="vep_options.html#opt_nearest">--nearest</a></li> <li><a href="vep_filter.html">filter_vep</a> supports field/field comparisons e.g. AFR_AF > #EUR_AF</li> <li>Exclude predicted (XM and XR) transcripts when using RefSeq or merged cache with <a href="vep_options.html#opt_exclude_predicted">--exclude_predicted</a></li> <li>Filter transcripts used for annotation with <a href="vep_options.html#opt_transcript_filter">--transcript_filter</a></li> <li>pileup input format no longer supported</li> </ul> </div> </div> <h4 id="old_vep_tool">Older versions (ensembl-tools) - until version 87: <a class="button" href="#old_vep_tool" onclick="show_hide('old_vep_tool');" id="a_old_vep_tool" style="font-weight:normal">Show</a></h4> <div id="div_old_vep_tool" style="display:none"> <p> Versions of VEP up to and including 87 were released as part of the ensembl-tools package. See <a href="#toolsversions">download links</a> above. </p> <h4> New in version 87 <i>(December 2016)</i> </h4> <ul> <li><a rel="external" href="https://github.com/Ensembl/ensembl-vep">Shiny new code</a> available for beta testing!</li> <li>Some minor speed optimisations</li> <li>Improve checks for valid chromosome names in input</li> <li><a rel="external" href="https://github.com/Ensembl/ensembl-vep#haplo">Haplosaurus</a> beta released - generate whole-transcript haplotype sequences from phased genotype data</li> </ul> <h4> New in version 86 <i>(October 2016)</i> </h4> <ul> <li>Chromosome synonyms supported when using VEP caches; may be loaded manually with <a href="vep_options.html#opt_synonyms">--synonyms</a></li> </ul> <h4> New in version 85 <i>(July 2016)</i> </h4> <ul> <li><a href="vep_options.html#opt_pick">--pick</a> now uses translated length instead of genomic transcript length</li> <li>Support for epigenomes in regulatory features</li> </ul> <h4> New in version 84 <i>(March 2016)</i> </h4> <ul> <li>Add <a href="/info/docs/tools/vep/vep_formats.html#tab">tab-delimited</a> output option</li> <li>Add <a href="/info/docs/tools/vep/vep_formats.html#output">transcript flags</a> indicating if the transcript is 5'- or 3'-incomplete</li> <li>Improve annotation of long variants where invariant parts of the alternate allele overlap splice regions</li> </ul> <h4> New in version 83 <i>(December 2015)</i> </h4> <ul> <li> Speed: <ul> <li>Basic consequence calculations up to 2x faster than version 82</li> <li>HGVS calculations up to 10x faster</li> <li>FASTA sequence retrieval implements caching</li> </ul> </li> <li>Add <a href="http://exac.broadinstitute.org/" rel="external">ExAC project</a> frequencies with <a href="vep_options.html#opt_af_exac">--af_exac</a></li> <li><a href="/Help/Glossary?id=521">APPRIS</a> isoform annotations now available with <a href="vep_options.html#opt_appris">--appris</a> and used by <a href="vep_options.html#opt_pick">--pick</a> and others to prioritise VEP annotations</li> </ul> <h4> New in version 82 <i>(September 2015)</i> </h4> <ul> <li><a href="#installer">Faster FASTA file access</a> using Bio::DB::HTS/htslib and bgzipped FASTA files</li> <li><a href="vep_options.html#opt_gene_phenotype">Flag genes</a> with phenotype associations</li> <li>Some plugins now available for use via the <a href="/Tools/VEP">web</a> and <a rel="external" href="http://rest.ensembl.org/#VEP">REST</a> interfaces</li> </ul> <h4> New in version 81 <i>(July 2015)</i> </h4> <ul> <li>Plugin registry means plugins can be installed from the <a href="#installer">VEP installer</a></li> <li>GFF format now supported by VEP's <a href="vep_cache.html#gtf">cache converter</a></li> <li>Fixes and improvements for sequence retrieval from FASTA files</li> </ul> <h4> New in version 80 <i>(May 2015)</i> </h4> <ul> <li><a href="../vep_formats.html#output">Flag added</a> indicating if an overlapping known variant is associated with a phenotype, disease or trait</li> <li>HGVS notations are now 3'-shifted by default (use <a href="vep_options.html#opt_shift_hgvs">--shift_hgvs</a> to force enable/disable)</li> <li>Source version information added to caches; see output file headers or use <a href="vep_options.html#opt_show_cache_info">--show_cache_info</a></li> <li>Get the variant class using <a href="vep_options.html#opt_variant_class">--variant_class</a></li> <li>CCDS status added to categories used by <a href="vep_options.html#opt_pick">--pick</a> flag (and <a href="vep_other.html#pick">others</a>)</li> </ul> <h4> New in version 79 <i>(March 2015)</i> </h4> <ul> <li>Focus on performance and stability: ~100% faster than version 78 and a new test suite</li> <li>New guide to <a href="vep_other.html#faster">getting VEP running faster</a></li> <li>1000 Genomes Phase 3 data available in GRCh37 cache download (GRCh38 coming soon, see <a href="vep_example.html#1kg_p3">docs</a> to access now)</li> <li><a href="../vep_formats.html#vcfout">VCF output</a> has changed slightly to match output from other tools</li> <li>Impact modifier added for each consequence type</li> </ul> <h4> New in version 78 <i>(December 2014)</i> </h4> <ul> <li>Customise <a href="vep_options.html#opt_pick">--pick</a> using <a href="vep_options.html#opt_pick_order">--pick_order</a></li> <li>Get <a href="/Help/Glossary?id=492">transcript support level</a> using <a href="vep_options.html#opt_tsl">--tsl</a></li> </ul> <h4> New in version 77 <i>(October 2014)</i> </h4> <ul> <li>Get the <a href="http://www.sequenceontology.org/" rel="external">SO</a> feature type of regulatory features using <a href="vep_options.html#opt_regulatory">--regulatory</a> and <a href="vep_options.html#opt_biotype">--biotype</a></li> </ul> <h4> New in version 76 <i>(August 2014)</i> </h4> <ul> <li>VEP now supports caches from multiple assemblies (<a href="vep_options.html#opt_assembly">--assembly</a>) on the same software version - e.g. <a href="vep_other.html#assembly">human builds GRCh37 and GRCh38</a></li> <li>Protein identifiers from UniProt (SWISSPROT, TrEMBL and UniParc) now available using <a href="vep_options.html#opt_uniprot">--uniprot</a></li> <li>VEP can generate <a href="../vep_formats.html#json">JSON output</a> using <a href="vep_options.html#opt_json">--json</a></li> <li>Two new analysis set options - <a href="vep_options.html#opt_gencode_basic">--gencode_basic</a> and the merged Ensembl/RefSeq cache (<a href="vep_options.html#opt_merged">--merged</a>)</li> <li>Non-RefSeq transcripts now excluded by default when using the RefSeq or merged cache; use <a href="vep_options.html#opt_all_refseq">--all_refseq</a> to include them</li> <li>Let VEP pick one consequence per variant allele using <a href="vep_options.html#opt_pick_allele">--pick_allele</a></li> <li>Allele now included alongside frequency for 1000 Genomes (<a href="vep_options.html#opt_af_1kg">--af_1kg</a>) and ESP (<a href="vep_options.html#opt_af_esp">--af_esp</a>) data</li> <li>Not strictly script-related, but the <a href="http://rest.ensembl.org/#Variation" rel="external">VEP REST API</a> has come out of beta!</li> </ul> <h4> New in version 75 <i>(February 2014)</i> </h4> <ul> <li>let VEP pick one consequence per variant for you using <a href="vep_options.html#opt_pick">--pick</a>; includes all transcript-specific data</li> <li><a href="vep_options.html#opt_symbol">gene symbol</a> available in RefSeq cache and when using <a href="vep_options.html#opt_refseq">--refseq</a></li> <li>Installation and use of RefSeq cache improved - remember to use <a href="vep_options.html#opt_refseq">--refseq</a> with your RefSeq cache!</li> <li>Added <a href="vep_options.html#opt_cache_version">--cache_version</a> option, primarily to aid Ensembl Genomes users.</li> </ul> <h4> New in version 74 <i>(December 2013)</i> </h4> <ul> <li>retrieve the <a href="http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview#prediction" rel="external">humDiv PolyPhen prediction</a> instead of humVar using <a href="vep_options.html#opt_humdiv">--humdiv</a></li> <li>source for gene symbol available with <a href="vep_options.html#opt_symbol">--symbol</a></li> </ul> <h4> New in version 73 <i>(August 2013)</i> </h4> <ul> <li>NHLBI-ESP frequencies available in cache (<a href="vep_options.html#opt_af_esp">--af_esp</a>)</li> <li>Pubmed IDs for cited existing variants available in cache (<a href="vep_options.html#opt_pubmed">--pubmed</a>)</li> <li><a href="vep_cache.html#convert">Convert your cache to use tabix</a> - much faster when retrieving co-located existing variants!</li> <li>The <a href="vep_download.html#installer">installer</a> can now update the VEP to the latest version and install <a href="vep_cache.html#fasta">FASTA files</a></li> <li><b>--hgnc</b> replaced by <a href="vep_options.html#opt_symbol">--symbol</a> for non-human compatibility</li> <li>HGVS strings are now part <a rel="external" href="http://en.wikipedia.org/wiki/Percent-encoding" rel="exeternal">URI-escaped</a> to avoid "=" sign clashes</li> <li>use <a href="vep_options.html#opt_allele_number">--allele_number</a> to identify input alleles by their order in the VCF ALT field</li> <li>use <a href="vep_options.html#opt_total_length">--total_length</a> to give the total length of cDNA, CDS and protein sequences</li> <li>add data from VCF INFO fields when using <a href="vep_custom.html">custom annotations</a></li> </ul> <h4> New in version 72 <i>(June 2013)</i> </h4> <ul> <li>Speed and stability improvements when using forking</li> <li>Filter VEP results using <a href="vep_filter.html">filter_vep.pl</a></li> </ul> <h4> New in version 71 <i>(April 2013)</i> </h4> <ul> <li>SIFT predictions now available for Chicken, Cow, Dog, Human, Mouse, Pig, Rat and Zebrafish</li> <li>View <a href="../vep_formats.html#stats">summary statistics</a> for VEP runs in [output]_summary.html</li> <li>Generate HTML output using <a href="vep_options.html#opt_html">--html</a></li> <li>Support for simple tab-delimited format for input of structural variant data</li> <li>Cache now contains clinical significance statuses from dbSNP for human variants</li> <li><p><b>NOTE:</b> VEP version numbers have now (from release 71) changed to match Ensembl release numbers.</p></li> </ul> <h4> New in version 2.8 <i>(December 2012)</i> </h4> <ul> <li>Easily filter out common human variants with <a href="vep_options.html#opt_filter_common">--filter_common</a></li> <li>1000 Genomes continental population frequencies now stored in cache files</li> </ul> <h4> New in version 2.7 <i>(October 2012)</i> </h4> <ul> <li>build VEP cache files offline from GTF and FASTA files</li> <li>support for using FASTA files for sequence lookup in HGVS notations in offline/cache modes</li> </ul> <h4> New in version 2.6 <i>(July 2012)</i> </h4> <ul> <li>support for <a href="../vep_formats.html#sv">structural variant</a> consequences</li> <li>Sequence Ontology (SO) consequence terms now default</li> <li>script runtime 3-4x faster when using <a href="vep_options.html#forking">forking</a></li> <li>1000 Genomes global MAF available in cache files</li> <li>improved memory usage</li> </ul> <h4> New in version 2.5 <i>(May 2012)</i> </h4> <ul> <li>SIFT and PolyPhen predictions now available for RefSeq transcripts</li> <li>retrieve cell type-specific regulatory consequences</li> <li>consequences can be retrieved based on a single individual's genotype in a VCF input file</li> <li>find overlapping structural variants</li> <li>Condel support removed from main script and moved to a plugin</li> </ul> <h4> New in version 2.4 <i>(February 2012)</i> </h4> <ul> <li>offline mode and new installer script make it easy to use the VEP without the usual dependencies</li> <li>output columns configurable using the <a href="vep_options.html#opt_fields">--fields</a> flag</li> <li>VCF output support expanded, can now carry all fields</li> <li>output affected exon and intron numbers with <a href="vep_options.html#opt_numbers">--numbers</a></li> <li>output overlapping protein domains using <a href="vep_options.html#opt_domains">--domains</a></li> <li>enhanced support for LRGs</li> <li>plugins now work on variants called as intergenic</li> </ul> <h4> New in version 2.3 <i>(December 2011)</i> </h4> <ul> <li>add custom annotations from tabix-indexed files (BED, GFF, GTF, VCF, bigWig)</li> <li>add new functionality to the VEP with user-written plugins</li> <li>filter input on consequence type</li> </ul> <h4> New in version 2.2 <i>(September 2011)</i> </h4> <ul> <li>SIFT, PolyPhen and Condel predictions and regulatory features now accessible from the <a href="vep_cache.html">cache</a></li> <li>support for calling consequences against <a href="vep_other.html#refseq">RefSeq</a> transcripts</li> <li>variant identifiers (e.g. dbSNP rsIDs) and <a href="vep_other.html#hgvs">HGVS notations</a> supported as input format</li> <li>variants can now be <a href="vep_options.html#filt">filtered</a> by frequency in HapMap and 1000 genomes populations</li> <li>script can be used to convert files between formats (Ensembl/VCF/Pileup/HGVS to Ensembl/VCF/Pileup)</li> <li>large amount of code moved to API modules to ensure consistency between web and script VEP</li> <li>memory usage optimisations</li> <li>VEP script moved to <a href="https://github.com/Ensembl/ensembl-tools/tree/release/113/scripts/variant_effect_predictor" rel="external">ensembl-tools repo</a></li> <li>Added <a href="vep_options.html#opt_canonical">--canonical</a>, <a href="vep_options.html#opt_per_gene">--per_gene</a> and <a href="vep_options.html#opt_no_intergenic">--no_intergenic</a> options</li> </ul> <h4> New in version 2.1 <i>(June 2011)</i> </h4> <ul> <li>ability to use local file <a href="vep_cache.html#cache">cache</a> in place of or alongside connecting to an Ensembl database</li> <li>significant improvements to speed of script</li> <li>whole-genome mode now default (no disadvantage for smaller datasets)</li> <li>improved status output with progress bars</li> <li>regulatory region consequences now reinstated and improved</li> <li>modification to output file - Transcript column is now Feature, and is followed by a Feature_type column</li> </ul> <h4> New in version 2.0 <i>(April 2011)</i> </h4> <ul> <li>support for SIFT, PolyPhen and Condel missense predictions in human</li> <li>per-allele and compound consequence types</li> <li>support for Sequence Ontology (SO) and NCBI consequence terms</li> <li> modified output format <ul> <li>support for new output fields in Extra column</li> <li>header section contains information on database and software versions</li> <li>codon change shown in output</li> <li>CDS position shown in output</li> <li>option to output Ensembl protein identifiers</li> <li>option to output HGVS nomenclature for variants</li> </ul> </li> <li>support for gzipped input files</li> <li>enhanced configuration options, including the ability to read configuration from a file</li> <li>verbose output now much more useful</li> <li>whole-genome mode now more stable</li> <li>finding existing co-located variations now ~5x faster</li> </ul> </div> <hr/> <h2 id="requirements">Requirements</h2> VEP requires: <ul> <li><b>gcc</b>, <b>g++</b> and <b>make</b></li> <li><b>Perl</b> version <b>5.10</b> or above recommended (tested on 5.10, 5.14, 5.18, 5.22, 5.26)</li> <li><b>Perl</b> packages: <ul> <li><a href="https://metacpan.org/pod/Archive::Zip" rel="external">Archive::Zip</a></li> <li><a href="https://metacpan.org/release/DVEEDEN/DBD-mysql-4.050/view/lib/DBD/mysql.pm" rel="external">DBD::mysql</a> (version <=4.050)</li> <li><a href="https://metacpan.org/pod/DBI" rel="external">DBI</a></li> </ul> See <a href="http://www.cpan.org/modules/INSTALL.html" rel="external">this guide</a> for more information on how to install perl modules.<br/> <a href="#additional">Additional libraries</a> can be installed for extra features and enhancements but they are not required to run VEP in most of the use cases. </li> </ul> <p>VEP's INSTALL.pl script will install required components of Ensembl API for you, but VEP may also be used with any pre-existing API installations you have, <b>provided their versions match the version of VEP you are using</b>. </p> <p>VEP is available in the following platforms:<p> <ul> <li>Linux (e.g., Ubuntu, Debian, Mint)</li> <li><a href="#macos">macOS</a></li> <li><a href="#windows"><img style="vertical-align:bottom" src="/i/16/windows.png"/> Windows</a> (requires a more involved installation process)</li> </ul> <p>VEP is also available as <a href="#docker">Docker</a> and <a href="#singularity">Singularity</a> images, allowing to skip the complex installation steps.</p> <hr/> <h2 id="installer">Installation</h2> <p> VEP's INSTALL.pl makes it easy to set up your environment for using the VEP. It will download and configure a minimal set of the Ensembl API for use by the VEP, and can also download <a href="vep_cache.html#cache">cache files</a>, <a href="vep_cache.html#fasta">FASTA files</a> and <a href="vep_plugins.html">plugins</a>. </p> <p>Run the following, and follow any prompts as they appear:</p> <pre class="code sh_sh">perl INSTALL.pl</pre> <p><a href="#additional">Additional non-essential components</a> and enhancements must be installed manually.</p> <br /> <h3> Software components installed </h3> <ul> <li><a href="https://github.com/bioperl/bioperl-live" rel="external">BioPerl</a></li> <li><a href="https://github.com/Ensembl/ensembl" rel="external">ensembl</a></li> <li><a href="https://github.com/Ensembl/ensembl-io" rel="external">ensembl-io</a></li> <li><a href="https://github.com/Ensembl/ensembl-variation" rel="external">ensembl-variation</a></li> <li><a href="https://github.com/Ensembl/ensembl-funcgen" rel="external">ensembl-funcgen</a></li> <li><a href="https://github.com/Ensembl/Bio-DB-HTS" rel="external">Bio::DB::HTS</a></li> </ul> <p> If you already have the latest version of the API installed you do not need to run the installer, although it can be used to simply update your API version (with post-release patches applied), and retrieve cache and FASTA files. The installer downloads the API within the VEP directory and will not affect any other Ensembl API installations. </p> <p> The script will also attempt to install a Perl::XS module, <a rel="external" href="https://github.com/Ensembl/Bio-HTS">Bio::DB::HTS</a>, for rapid access to bgzipped FASTA files. If this fails, you may add the --NO_HTSLIB flag when running the installer; VEP will fall back to using Bio::DB::Fasta for this functionality (<a href="vep_cache.html#fasta">more details</a>).</p> <br /> <h3 id="run_install">Running the installer</h2> <p> The installer is run on the command line as follows: </p> <pre class="code sh_sh"> perl INSTALL.pl [options] </pre> <p> Follow on-screen prompts and note warnings of any files which will be deleted/overwritten</p> <p> You should not need to add any options, but configuration of the installer is possible with the flags below. Options can also be set by exporting <b>environment variables</b> prefixed with <kbd>VEP_</kbd> before running the installer (for instance, <kbd>export VEP_NO_HTSLIB=1</kbd> and <kbd>export VEP_DIR_PLUGINS="/plugins"</kbd>).</p> <table class="ss"> <tr> <th>Flag</th> <th>Alternate</th> <th>Description</th> </tr> <tr id="opt_assembly"> <td><pre>--ASSEMBLY</pre></td> <td><pre>-y</pre></td> <td> Assembly version to use when using <code>--AUTO</code>. Most species have only one assembly available on each software release; currently this is only required for <a href="vep_other.html#assembly">human on release 76</a> onwards. </td> </tr> <tr id="opt_auto"> <td><pre>--AUTO</pre></td> <td><pre>-a</pre></td> <td> Run installer without prompts. Use the following options to specify parts to install: <ul> <li><b>a</b> (API + Bio::DB::HTS/htslib)</li> <li><b>l</b> (Bio::DB::HTS/htslib only)</li> <li><b>c</b> (cache)</li> <li><b>f</b> (FASTA)</li> <li><b>p</b> (plugins) — Require the use of the <a href="#opt_plugins">--PLUGINS</a> flag to list the plugin(s) to install.</li> </ul> <p>e.g. for API and cache:</p> <pre class="code sh_sh">perl INSTALL.pl --AUTO ac</pre> </td> </tr> <tr id="opt_cache_version"> <td><pre>--CACHE_VERSION [version]</pre></td> <td> </td> <td> By default the installer will download the latest version of VEP caches and FASTA files (currently 113). You can force the script to install a different version, but there is no guarantee that a version of the API will be compatible with a different version of the cache. </td> </tr> <tr id="opt_cachedir"> <td><pre>--CACHEDIR [dir]</pre></td> <td><pre>-c</pre></td> <td> <p>By default the script will install the cache files in the ".vep" subdirectory in your home area. This option configures where cache files are installed.</p> <p>The <a href="vep_options.html#opt_dir_cache">--dir_cache</a> flag must be passed when running the VEP if a non-default cache directory is given:</p> <pre class="code sh_sh">./vep --dir_cache [dir]</pre> </td> </tr> <tr id="opt_destdir"> <td><pre>--DESTDIR [dir]</pre></td> <td><pre>-d</pre></td> <td> <p>By default the script will install the API modules in a subdirectory of the current directory named "Bio". Using this option you can configure where the Bio directory is created. If something other than the default is used, this directory must either be added to your PERL5LIB environment variable when running the VEP, or included using perl's -I flag:</p> <pre class="code sh_sh">perl -I [dir] vep</pre> </td> </tr> <tr id="opt_no_htslib"> <td><pre>--NO_HTSLIB</pre></td> <td><pre>-l</pre></td> <td>Don't attempt to install Bio::DB::HTS/htslib</td> </tr> <tr id="opt_no_test"> <td><pre>--NO_TEST</pre></td> <td> </td> <td>Don't run API tests - useful if you know a harmless failure will prevent continuation of the installer</td> </tr> <tr id="opt_no_update"> <td><pre>--NO_UPDATE</pre></td> <td><pre>-n</pre></td> <td> By default the script will check for new versions or updates of the VEP. Using this option will skip this check. </td> </tr> <tr id="opt_plugins"> <td><pre>--PLUGINS</pre></td> <td><pre>-g</pre></td> <td> <p>Comma-separated list of plugins to install when using <code>--AUTO</code>. To install all available plugins, use <code>--PLUGINS all</code>.</p> <pre class="code sh_sh"># List the available plugins: perl INSTALL.pl -a p --PLUGINS list # Download/install all the available plugins: perl INSTALL.pl -a p --PLUGINS all # Download/install a defined list of plugins, e.g.: perl INSTALL.pl -a p --PLUGINS dbNSFP,CADD,G2P</pre> </td> </tr> <tr id="opt_pluginsdir"> <td><pre>--PLUGINSDIR [dir]</pre></td> <td><pre>-r</pre></td> <td> <p>By default the script will install the plugins files in the "Plugins" subdirectory of the <code>--CACHEDIR</code> directory. This option configures where the plugins files are installed.</p> <p>The <a href="vep_options.html#opt_dir_plugins">--dir_plugins</a> flag must be passed when running the VEP if a non-default plugins directory is given:</p> <pre class="code sh_sh">./vep --dir_plugins [dir]</pre> </td> </tr> <tr id="opt_prefer_bin"> <td><pre>--PREFER_BIN</pre></td> <td><pre>-p</pre></td> <td>Use this if the installer fails with out of memory errors.</td> </tr> <tr id="opt_species"> <td><pre>--SPECIES</pre></td> <td><pre>-s</pre></td> <td> <p>Comma-separated list of species to install when using <code>--AUTO</code>. To install the RefSeq cache, add "_refseq" to the species name, e.g. "homo_sapiens_refseq", or "_merged" to install the merged Ensembl/RefSeq cache. Remember to use <a href="vep_options.html#opt_refseq">--refseq</a> or <a href="vep_options.html#opt_merged">--merged</a> when running the VEP with the relevant cache!</p> <p>Use <code>all</code> to install data for all available species.</p> </td> </tr> <tr id="opt_quiet"> <td><pre>--QUIET</pre></td> <td><pre>-q</pre></td> <td>Don't write any status output when using <code>--AUTO</code>.</td> </tr> </table> <hr/> <h2 id="additional">Additional components</h2> <p> INSTALL.pl will set up the minimum requirements for VEP. Some features and enhancements, however, require the installation of additional components. Most are perl modules that are easily installed using cpanm; see <a href="http://www.cpan.org/modules/INSTALL.html" rel="external">this guide</a> for more information on how to install perl modules. </p> <p> Typically, you will use cpanm to install modules locally in your home directories; this shows how to set up a path for perl modules and install one there: </p> <pre class="code sh_sh">mkdir -p $HOME/cpanm export PERL5LIB=$PERL5LIB:$HOME/cpanm/lib/perl5 cpanm -l $HOME/cpanm Set::IntervalTree</pre> <p> To make the change to <code>PERL5LIB</code> permanent, it is recommended to add the <code>export</code> line to your <code>$HOME/.bashrc</code> or <code>$HOME/.profile</code>. </p> <ul> <li> Additional features <ul> <li><a href="http://search.cpan.org/dist/JSON/" rel="external">JSON</a> - required to produce <a href="vep_options.html#opt_json">JSON format output</a></a></li> <li><a href="http://search.cpan.org/~benbooth/Set-IntervalTree/lib/Set/IntervalTree.pm" rel="external">Set::IntervalTree</a> - used to find overlaps between entities in coordinate space. Required to use <a href="vep_options.html#opt_nearest">--nearest</a></li> <li><a href="http://search.cpan.org/~lds/Bio-BigFile-1.07/lib/Bio/DB/BigFile.pm" rel="external">Bio::DB::BigFile</a> - required to use bigWig format <a href="vep_custom.html">custom annotation files</a>. See <a href="#bigfile">Bio::DB::BigFile instructions</a>.</li> </ul> </li> <li> Speed enhancements - these modules can improve VEP runtime <ul> <li><a href="http://search.cpan.org/~nwclark/PerlIO-gzip-0.19/gzip.pm">PerlIO::gzip</a> - marginal gains in compressed file parsing as used by VEP cache</li> <li><a href="https://github.com/Ensembl/ensembl-xs" rel="external">ensembl-xs</a> - provides pre-compiled replacements for frequently used routines in VEP. Requires manual installation, see <a href="https://github.com/Ensembl/ensembl-xs" rel="external">README</a> for details</li> </ul> </li> </ul> <br /> <h3 id="bigfile">Bio::DB::BigFile</h3> <p> In order for VEP to be able to access bigWig format custom annotation files, the Bio::DB::BigFile perl module is required. Installation involves downloading and compiling the <a href="https://github.com/ucscGenomeBrowser/kent" rel="external">kent source tree</a>. The current version of the kent source tree does not work correctly with Bio::DB::BigFile, so it is necessary to install an archive version known to work (v335). </p> <ol> <li> <p>Download and unpack the kent source tree</p> <pre class="code sh_sh">wget https://github.com/ucscGenomeBrowser/kent/archive/v335_base.tar.gz tar xzf v335_base.tar.gz</pre> </li> <li> <p>Set up some environment variables; these are required only temporarily for this installation process</p> <pre class="code sh_sh">export KENT_SRC=$PWD/kent-335_base/src export MACHTYPE=$(uname -m) export CFLAGS="-fPIC" export MYSQLINC=`mysql_config --include | sed -e 's/^-I//g'` export MYSQLLIBS=`mysql_config --libs`</pre> </li> <li> <p>Modify kent build parameters</p> <pre class="code sh_sh">cd $KENT_SRC/lib echo 'CFLAGS="-fPIC"' > ../inc/localEnvironment.mk</pre> </li> <li> <p>Build kent source</p> <pre class="code sh_sh">make clean && make cd ../jkOwnLib make clean && make</pre> <p>If either of these steps fail, you may have some missing dependencies. Known common missing dependencies are libpng and libssl; these may be installed, for example, with <code>apt-get</code> on Ubuntu. If you do not have sudo access you may have to ask your sysadmin to install any missing dependencies.</p> <pre class="code sh_sh">sudo apt-get install libpng-dev libssl-dev</pre> <p>On macOS you may use <a href="https://brew.sh/" rel="external"><code>brew</code></a>; the openssl libraries also need to be symbolically linked to a different path:</p> <pre class="code sh_sh">brew install libpng openssl cd /usr/local/include ln -s ../opt/openssl/include/openssl . cd -</pre> </li> <li> <p>On some systems (e.g. macOS), a compiled file is placed in a path that Bio::DB::BigFile cannot find. You can correct this with:</p> <pre class="code sh_sh">ln -s $KENT_SRC/lib/x86_64/* $KENT_SRC/lib/</pre> </li> <li> <p>We'll now use cpanm to install the perl module for Bio::DB::BigFile itself. See <a href="#additional">above</a> for guidance on this. In this example we're going to install the module to a path within your home directory. In order to do this we must modify the paths that perl looks in to find modules by adding to the <code>PERL5LIB</code> environment module. To make this change permanent you must add the <code>export</code> line to your <code>$HOME/.bashrc</code> or <code>$HOME/.profile</code>.</p> <pre class="code sh_sh">mkdir -p $HOME/cpanm export PERL5LIB=$PERL5LIB:$HOME/cpanm/lib/perl5 cpanm -l $HOME/cpanm Bio::DB::BigFile</pre> <p>If you are prompted for the path to the kent source tree, that means something didn't go right in the compilation above. Double check that <code>$KENT_SRC/lib/jkweb.a</code> exists and is not found instead at e.g. <code>$KENT_SRC/lib/x86_64/jkweb.a</code>. You may copy or link the file (and the other files in that directory) to the former path.</p> <pre class="code sh_sh">ln -s $KENT_SRC/lib/x86_64/* $KENT_SRC/lib/</pre> </li> <li> <p>You should now be able to successfully run the appropriate test in the VEP package:</p> <pre class="code sh_sh">perl -Imodules t/AnnotationSource_File_BigWig.t</pre> </li> </ol> <hr/> <h2 id="macos">Using VEP in macOS</h2> <p>Installing VEP on macOS is slightly trickier than other Linux-based systems, and will require additional dependancies.<br /> These instructions will guide you through the setup of <b>Perlbrew</b>, <b>Homebrew</b>, <b>MySQL</b> and other dependancies that will allow for a clean installation of VEP on your macOS system.</p> <p>These instructions have been tested on <b>macOS High Sierra (10.13)</b> and <b>macOS Sierra (10.12)</b>.<br />Older versions may require additional tweaks, however we shall endeavouXcoder to keep these instructions up to date for future versions of MacOS.</p> <div> <div style="float:left" class="warning"> <h3 id="apple_silicon_macs">Installation issues with M-series Macs</h3> <div class="message-pad"> <p>We advise using the <a href="#docker">Docker</a> or <a href="#singularity">Singularity</a> images for VEP if you are having issues installing VEP in Apple Silicon (M1, M2, etc.) Macs.</p> </div> </div> <div class="clear"></div> </div> <br /> <h3>Prerequisite Setup</h3> <p>List of prerequisites: <b>Xcode</b>, <b>GCC</b>, <b>Perlbrew</b>, <b>Cpanm</b>, <b>Homebrew</b>, <b>mysql</b>, <b>DBI</b>, <b>DBD::mysql</b> (version <=4.050)</p> <h4>Xcode and GCC</h4> <p>VEP requires Xcode and GCC for installation purposes. Fortunately, recent versions of macOS will look for (and attempt to install if required) both of these when you run the following command:</p> <pre class="code sh_sh">gcc -v</pre> <h4>Perlbrew</h4> <p>We recommend using Perlbrew to install a new version of Perl on your mac, to prevent messing with the vendor perl too much. This can be done with the following command:</p> <pre class="code sh_sh">curl -L http://install.perlbrew.pl | bash echo 'source $HOME/perl5/perlbrew/etc/bashrc' >> ~/.bash_profile</pre> <p>At this point, PLEASE RESTART YOUR TERMINAL WINDOW to allow for the perlbrew changes to take effect.</p> <p>We recommend installing Perl version <b>5.26.2</b> to run VEP, and installing cpanm to handle the installation of perl modules.<br /> These steps can be completed with the commands:</p> <pre class="code sh_sh">perlbrew install -j 5 --as 5.26.2 --thread --64all -Duseshrplib perl-5.26.2 --notest perlbrew switch 5.26.2 perlbrew install-cpanm</pre> <h4>Homebrew</h4> <p>This package management system for macOS would make the installation of the next prerequisite (i.e. xs) easier.</p> <pre class="code sh_sh">/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"</pre> <h4>xz</h4> <p>VEP requires the installation of xz, a data-compression utility. The easiest way to install the xz package is through homebrew:</p> <pre class="code sh_sh">brew install xz</pre> <h4>MySQL</h4> <p>In order to connect to the Ensembl databases, a collection of MySQL related dependancies are required. Fortunately, these can be installed neatly with <b>Homebrew</b> and <b>Cpanm</b>:</p> <pre class="code sh_sh">brew install mysql cpanm DBI cpanm DBD::mysql@4.050</pre> <br /> <h3>Installing BioPerl</h3> <p>On some versions of macOS, the VEP installer fails to cleanly install BioPerl, so a manual install will prevent issues:</p> <pre class="code sh_sh">curl -O https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz tar zxvf BioPerl-1.6.924.tar.gz echo 'export PERL5LIB=${PERL5LIB}:##PATH_TO##/bioperl-1.6.924' >> ~/.bash_profile</pre> <p> where <i>##PATH_TO##/bioperl-1.6.924</i> refers to the location of the newly unzipped BioPerl directory.</p> <br /> <h3>Final Dependancies</h3> <p>Installing the following Perl modules with cpanm will allow for full VEP functionality:</p> <pre class="code sh_sh">cpanm Test::Differences Test::Exception Test::Perl::Critic Archive::Zip PadWalker Error Devel::Cycle Role::Tiny::With Module::Build export DYLD_LIBRARY_PATH=/usr/local/mysql/lib/:$DYLD_LIBRARY_PATH</pre> <br /> <h3>Installing VEP</h3> <p>And that should be that! You should now be able to install VEP using the installer:</p> <pre class="code sh_sh">git clone https://github.com/ensembl/ensembl-vep cd ensembl-vep perl INSTALL.pl --NO_TEST</pre> <hr/> <h2 id="windows">Using VEP in Windows <img style="padding-left:2px" src="/i/16/windows.png"/></h2> <p> VEP was developed as a command-line tool, and as a Perl script its natural environment is a Linux system. However, there are several ways you can use VEP on a Windows machine. </p> <p> You may also consider using VEP's web or REST interfaces. </p> <br /> <h4 id="virtual">Virtual machines</h4> <p> Using a virtual machine you can run a virtual Linux system in a window on your machine. There are two ways to do this: </p> <ol> <li>Use the <a href="/info/data/virtual_machine.html">Ensembl virtual machine image</a></li> <li>Use <a href="#docker">Docker</a></li> </ol> <br /> <h4 id="wperl">Perl</h4> <p> If Perl is installed on Windows, VEP can be setup. However this may require installation of dependent modules. We recommend using <a href="#docker">Docker</a> to run VEP on Windows. </p> <ol> <li>Check Perl is installed</a></li> <li>Download and unpack the <a href="https://github.com/Ensembl/ensembl-vep/archive/release/113.zip">zip of the ensembl-vep package</a></li> <li>Open a Command Prompt (search for Command Prompt in the Start Menu)</li> <li> <p>Navigate to the directory where you unpacked the VEP package, e.g.</p> <pre class="code sh_sh">cd Downloads/ensembl-vep-release-113</pre> </li> <li> <p>Run INSTALL.pl with --NO_HTSLIB and --NO_TEST; you will see some warnings about the "which" command not being available (these will also appear when running VEP and can be ignored).</p> <pre class="code sh_sh">perl INSTALL.pl --NO_HTSLIB --NO_TEST</pre> </li> </ol> <hr/> <h2 id="docker">Docker</h2> <p> <a href="https://www.docker.com/" rel="external">Docker</a> allows running applications in virtualised <i>containers</i>. The VEP Docker image is available from DockerHub: <a class="button" href="https://hub.docker.com/r/ensemblorg/ensembl-vep/" target="_blank">VEP in DockerHub</a></p> <p>After installing <a href="https://www.docker.com/" rel="external">Docker</a>, download the VEP Docker image:</p> <pre class="code sh_sh">docker pull ensemblorg/ensembl-vep</pre> <p> To download cache files and other data with VEP Docker, we recommend <a href="https://docs.docker.com/engine/tutorials/dockervolumes/" rel="external">mounting a directory</a> from your local (host) machine to folder <code>/data</code> from the Docker image. For instance: </p> <pre class="code sh_sh"> mkdir $HOME/vep_data docker run -t -i -v $HOME/vep_data:/data ensemblorg/ensembl-vep</pre> <p> In the example above, data in <code>$HOME/vep_data</code> will be accessible by both the local machine and VEP Docker. The Ensembl VEP API, plugins and their dependencies (e.g. Perl APIs, Bio::DB::HTS, htslib, ...) are already installed in the image. </p> <div> <div style="float:left" class="warning"> <h3 id="read_write_access">Read/Write access from the container</h3> <div class="message-pad"> <p>In some distributions (e.g. CentOS, Fedora, Red Hat Enterprise Linux) Docker daemon requires <b>root</b> privileges (i.e. needs to prefix the command with <b>sudo</b>), which might cause read/write issues to the mounted volume.</p> <p>One solution is to use the option <b>:Z</b> within the Docker <b>-v</b> option (only from docker 1.7.0): <pre class="code sh_sh">sudo docker run -t -i -v $HOME/vep_data:/data:Z ensemblorg/ensembl-vep</pre> </p> <p>An other solution is to change the read/write access of the mounted volume (<code>$HOME/vep_data</code>): <pre class="code sh_sh">chmod -R a+rwx $HOME/vep_data</pre> </p> </div> </div> <div class="clear"></div> </div> <br /> <h3 id="docker_cache">Cache and FASTA files installation</h3> <p> You can run the INSTALL.pl script to install the cache and FASTA files: </p> <pre class="code sh_sh">docker run -t -i -v $HOME/vep_data:/data ensemblorg/ensembl-vep INSTALL.pl</pre> <ul> <li> You will be asked to install cache data. Type the comma-separated numbers for the species/assembly of interest and press <kbd>enter</kbd>. Your data will download and unpack; this may take a while. </li> <li> If you wish to retrieve HGVS annotations, please download the FASTA files for your species. To do this, at the next prompt type <kbd>0</kbd> and press <kbd>enter</kbd>. </li> </ul> <p> The above process may also be performed in one command; for example, to set up the cache and corresponding FASTA for human GRCh38: </p> <pre class="code sh_sh">docker run -t -i -v $HOME/vep_data:/data ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38</pre> <p> The installer downloads VEP data to the mounted directory (e.g., <code>$HOME/vep_data</code>). The downloaded data will be automatically detected as long as its folder is mounted when running VEP: </p> <pre class="code sh_sh">docker run -v $HOME/vep_data:/data ensemblorg/ensembl-vep vep -i examples/homo_sapiens_GRCh38.vcf --cache</pre> <br /> <h3 id="docker_setup">Running VEP with data from local folder</h3> <p>Here is an example on running VEP with data from folder <code>$HOME/vep_data</code> in the local machine (provided that the cache has been downloaded to that folder):</p> <pre class="code sh_sh"> docker run -v $HOME/vep_data:/data ensemblorg/ensembl-vep \ vep --cache --offline --format vcf --vcf --force_overwrite \ --input_file input/my_input.vcf \ --output_file output/my_output.vcf \ --custom file=custom/my_extra_data.bed,short_name=BED_DATA,format=bed,type=exact,coords=1 \ --plugin NMD</pre> <p>Please avoid using absolute paths to data as the paths inside the container differ from your local machine.</p> <br /> <h3>Update from a previous version</h3> <ol> <li><p>Update your Docker container</p> <pre class="code sh_sh"> docker pull ensemblorg/ensembl-vep</pre> </li> <li><p>Update your cache</p> <pre class="code sh_sh"># Install the new cache through the VEP INSTALL.pl script (see "Cache installation" section above) docker run -t -i -v $HOME/vep_data:/data ensemblorg/ensembl-vep INSTALL.pl -a c # Or install the cache manually cd $HOME/vep_data curl -O https://ftp.ensembl.org/pub/release-113/variation/vep/homo_sapiens_vep_113_GRCh38.tar.gz tar xzf homo_sapiens_vep_113_GRCh38.tar.gz</pre> </li> </ol> </div> <hr/> <h2 id="singularity">Singularity</h2> <p> Due to root requirements for the Docker daemon, using the <a href="https://hub.docker.com/r/ensemblorg/ensembl-vep/" rel="external">Docker container for VEP</a> is not always possible to HPC users. Singularity, an alternative containerisation tool, does not assume that you have a system where you are the root user. This has led to increased popularity in HPC contexts due to increased access rights flexibility. </p> <p>After installing <a href="https://sylabs.io/singularity/" rel="external">Singularity</a>, VEP may be used with Singularity based on the VEP Docker image from DockerHub:</p> <pre class="code sh_sh">singularity pull --name vep.sif docker://ensemblorg/ensembl-vep</pre> <p> The following is a brief example showing how to use a directory on your local (host) machine to store cache data for VEP. </p> <pre class="code sh_sh"> mkdir $HOME/vep_data singularity exec vep.sif vep --dir $HOME/vep_data --help</pre> <p> The Ensembl VEP API, plugins and their dependencies (e.g. Perl APIs, Bio::DB::HTS, htslib, ...) are already installed in the image. </p> <br /> <h3 id="singularity_cache">Cache and FASTA files installation</h3> <p> You can run the INSTALL.pl script to install the Cache data and FASTA files. For example, to set up the cache and corresponding FASTA for human GRCh38 in your local folder <code>$HOME/vep_data</code>: </p> <pre class="code sh_sh">singularity exec vep.sif INSTALL.pl -c $HOME/vep_data -a cf -s homo_sapiens -y GRCh38</pre> <p> The installer downloads data to the specified directory (e.g., <code>$HOME/vep_data</code>). When running VEP via Singularity, point to this directory using <code>--dir</code>: </p> <pre class="code sh_sh">singularity exec vep.sif vep --dir $HOME/vep_data -i examples/homo_sapiens_GRCh38.vcf --cache</pre> <br /> <h3 id="singularity_setup">Running VEP with data from local folder</h3> <p>Here is an example on running VEP with data from folder <code>$HOME/vep_data</code> in the local machine (provided that the cache has been downloaded to that folder):</p> <pre class="code sh_sh"> singularity exec vep.sif \ vep --dir $HOME/vep_data \ --cache --offline --format vcf --vcf --force_overwrite \ --input_file input/my_input.vcf \ --output_file output/my_output.vcf \ --custom file=custom/my_extra_data.bed,short_name=BED_DATA,format=bed,type=exact,coords=1 \ --plugin NMD</pre> <br /> <h3>Update from a previous version</h3> <ol> <li><p>Update your docker container</p> <pre class="code sh_sh">singularity pull --name vep.sif docker://ensemblorg/ensembl-vep</pre> </li> <li><p>Update your cache</p> <pre class="code sh_sh"># Install the new cache through the VEP INSTALL.pl script (see "Cache installation" section above) singularity exec vep.sif INSTALL.pl -c $HOME/vep_data -a c # Or install the cache manually cd $HOME/vep_data curl -O https://ftp.ensembl.org/pub/release-113/variation/vep/homo_sapiens_vep_113_GRCh38.tar.gz tar xzf homo_sapiens_vep_113_GRCh38.tar.gz</pre> </li> </ol> </div> </div> </div> </div></div> </div> <div id="footer"> <div class="column-wrapper"> <div class="column-two left"> <p>Ensembl release 113 - October 2024 © <span class="print_hide"><a href="http://www.ebi.ac.uk/" class="nowrap constant">EMBL-EBI</a></span> <span class="screen_hide_inline">EMBL-EBI<br />http://useast.ensembl.org</span> </p> </div> <div class="column-two right print_hide"><p> <a class="modal_link" id="p_link" href="/Help/Permalink?url=http%3A%2F%2FOct2024.archive.ensembl.org">Permanent link</a> </p></div> <p class="invisible">.</p> </div> <div class="column-wrapper"><hr /><div 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value=Hippocampus_comes|Mus_musculus_DBA_2J|Mus_musculus_NZO_HlLtJ|Pan_troglodytes|Sus_scrofa_bamei|Labrus_bergylta|Ovis_aries_white_dorper|Camelus_dromedarius|Ovis_aries_texel|Anser_cygnoides|Strigops_habroptila|Pelodiscus_sinensis|Salmo_salar_european_origin_alta|Choloepus_hoffmanni|Cyprinus_carpio_carpio|Gallus_gallus_GCA_016700215.2|Panthera_tigris_altaica|Nothoprocta_perdicaria|Ovis_aries_polled_dorset|Piliocolobus_tephrosceles|Anabas_testudineus|Cervus_hanglu_yarkandensis|Electrophorus_electricus|Amphiprion_percula|Myripristis_murdjan|Equus_asinus|Cyprinus_carpio_huanghe|Sander_lucioperca|Astyanax_mexicanus|Zosterops_lateralis_melanops|Chelonoidis_abingdonii|Monopterus_albus|Sus_scrofa_duroc|Parambassis_ranga|Gopherus_evgoodei|Loxodonta_africana|Erinaceus_europaeus|Amphiprion_ocellaris|Oreochromis_niloticus|Bos_mutus|Mustela_putorius_furo|Capra_hircus_xinong_saanen_dairy|Felis_catus|Kryptolebias_marmoratus|Sus_scrofa_meishan_GCA_017957985.1|Denticeps_clupeoides|Oryzias_latipes_hsok|Danio_rerio|Panthera_leo|Oncorhynchus_mykiss|Tupaia_belangeri|Cyprinus_carpio_hebao_red|Rattus_norvegicus_SHRUtx|Neovison_vison|Sus_scrofa_tibetan|Balaenoptera_musculus|Dasypus_novemcinctus|Apteryx_haastii|Ursus_maritimus|Coturnix_japonica|Catagonus_wagneri|Salvator_merianae|Numida_meleagris|Scleropages_formosus|Mus_musculus|Nothobranchius_furzeri|Lates_calcarifer|Corvus_moneduloides|Ursus_americanus|Phocoena_sinus|Poecilia_reticulata|Sphaeramia_orbicularis|Stachyris_ruficeps|Sus_scrofa_ningxiang|Pteropus_vampyrus|Pan_paniscus|Canis_lupus_familiaris|Zonotrichia_albicollis|Cavia_porcellus|Otus_sunia|Sorex_araneus|Equus_caballus|Sinocyclocheilus_rhinocerous|Sus_scrofa_pb115|Canis_lupus_familiarisboxer|Naja_naja|Sus_scrofa_hampshire|Vulpes_vulpes|Amphilophus_citrinellus|Scophthalmus_maximus|Prolemur_simus|Tetraodon_nigroviridis|Podarcis_muralis|Ovis_aries_chinese_merino|Carlito_syrichta|Buteo_japonicus|Papio_anubis|Pogona_vitticeps|Cottoperca_gobio|Ursus_thibetanus_thibetanus|Mus_musculus_A_J|Fukomys_damarensis|Callithrix_jacchus|Fundulus_heteroclitus|Terrapene_carolina_triunguis|Apteryx_rowi|Capra_hircus_saanen_dairy|Sus_scrofa_usmarc|Gasterosteus_aculeatus_marine_syl|Erythrura_gouldiae|Canis_lupus_familiarisgreatdane|Zalophus_californianus|Ictidomys_tridecemlineatus|Ailuropoda_melanoleuca|Rattus_norvegicus|Mus_musculus_AKR_J|Mus_musculus_129S1_SvImJ|Cyanistes_caeruleus|Anas_zonorhyncha|Marmota_marmota_marmota|Gorilla_gorilla|Xiphophorus_maculatus|Macaca_nemestrina|Camarhynchus_parvulus|Ovis_aries_east_friesian|Sinocyclocheilus_anshuiensis|Aquila_chrysaetos_chrysaetos|Mus_musculus_WSB_EiJ|Poecilia_latipinna|Laticauda_laticaudata|Saimiri_boliviensis_boliviensis|Lynx_canadensis|Accipiter_nisus|Jaculus_jaculus|Lepisosteus_oculatus|Pundamilia_nyererei|Capra_hircus|Bos_taurus_hybrid|Meleagris_gallopavo|Colobus_angolensis_palliatus|Chelydra_serpentina|Macaca_mulatta|Mus_musculus_NOD_ShiLtJ|Mus_musculus_FVB_NJ|Gouania_willdenowi|Bos_taurus|Pseudonaja_textilis|Ochotona_princeps|Mus_musculus_C57BL_6NJ|Chrysolophus_pictus|Suricata_suricatta|Apteryx_owenii|Gasterosteus_aculeatus_marine_bam|Octodon_degus|Astatotilapia_calliptera|Carassius_auratus|Caenorhabditis_elegans|Monodon_monoceros|Bison_bison_bison|Canis_lupus_familiarisbasenji|Sus_scrofa_jinhua|Anas_platyrhynchos_platyrhynchos|Nomascus_leucogenys|Ovis_aries_hu|Calidris_pugnax|Takifugu_rubripes|Rhinopithecus_roxellana|Paramormyrops_kingsleyae|Sinocyclocheilus_grahami|Struthio_camelus_australis|Erpetoichthys_calabaricus|Anas_platyrhynchos|Poecilia_mexicana|Callorhinchus_milii|Monodelphis_domestica|Meriones_unguiculatus|Rhinolophus_ferrumequinum|Sus_scrofa_berkshire|Seriola_lalandi_dorsalis|Mus_musculus_C3H_HeJ|Rattus_norvegicus_WKYBbb|Gopherus_agassizii|Cairina_moschata_domestica|Manacus_vitellinus|Strix_occidentalis_caurina|Sciurus_vulgaris|Mus_musculus_LP_J|Catharus_ustulatus|Pavo_cristatus|Echinops_telfairi|Mola_mola|Eptatretus_burgeri|Cebus_imitator|Oryzias_sinensis|Anolis_carolinensis|Gadus_morhua|Neogobius_melanostomus|Oryzias_javanicus|Panthera_pardus|Oreochromis_aureus|Notamacropus_eugenii|Sus_scrofa_nihs_2020|Urocitellus_parryii|Mus_musculus_PWK_PhJ|Ficedula_albicollis|Mesocricetus_auratus|Serinus_canaria|Ovis_aries_rambouillet|Latimeria_chalumnae|Anser_brachyrhynchus|Macaca_fascicularis|Pongo_abelii|Maylandia_zebra|Gallus_gallus|Stegastes_partitus|Spermophilus_dauricus|Gallus_gallus_GCA_000002315.5|Calidris_pygmaea|Geospiza_fortis|Amazona_collaria|Delphinapterus_leucas|Salmo_trutta|Bos_grunniens|Myotis_lucifugus|Mus_caroli|Phascolarctos_cinereus|Ornithorhynchus_anatinus|Mandrillus_leucophaeus|Peromyscus_maniculatus_bairdii|Saccharomyces_cerevisiae|Echeneis_naucrates|Oryctolagus_cuniculus|Periophthalmus_magnuspinnatus|Cavia_aperea|Ovis_aries_kermani|Sus_scrofa_ossabaw_miniature|Drosophila_melanogaster|Oryzias_latipes_hni|Salmo_salar_north_american_atlantic_salmon|Sphenodon_punctatus|Mus_musculus_CAST_EiJ|Chlorocebus_sabaeus|Physeter_catodon|Haplochromis_burtoni|Pygocentrus_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