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<h1>Variant Effect Predictor</h1>
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      <a href="/[[SPECIESDEFS::ENSEMBL_PRIMARY_SPECIES]]/UserData/UploadVariations" class="modal_link">
      <img src="/i/vep_logo_sm.png" title="Launch the online VEP!" alt="Variant Effect Predictor" /></a>

<p>The VEP determines the effect of your polymorphisms on genes, transcripts, 
and protein sequence.  Simply input the genomic coordinates of SNPs, insertions 
or deletions, along with any nucleotides at those positions, and export:</p>
<ul>
<li>genes affected by the changes</li>
<li>where the variants are located with respect to cDNAs (e.g. upstream, 
downstream, in the coding sequence)</li>
<li>if the substitutions, insertions or deletions have changed the protein sequence</li>
<li>SIFT and PolyPhen scores, if the protein sequence is changed</li>
</ul>
      <p class="center"><a
href="/[[SPECIESDEFS::ENSEMBL_PRIMARY_SPECIES]]/UserData/UploadVariations"
class="modal_link"><strong><i>Launch the online VEP tool!</i></strong></a></p>
<h2>Sample output</h2>
<p><img src="/i/help/vep_output.jpg" title="Sample VEP results table" alt="screenshot" /></p>

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<h2>How to access the Variant Effect Predictor</h2>
<p>
Ensembl provides the facility to predict the functional consequences of known and unknown variants
using the Variant Effect Predictor (VEP). There are three primary ways to use
the functionality of the VEP:
</p>

<ul>
  <li> through the web interface | <a href="#web">Documentation</a> | <a
href="/[[SPECIESDEFS::ENSEMBL_PRIMARY_SPECIES]]/UserData/UploadVariations"
class="modal_link">Launch web interface</a></li>
  <li> using the standalone perl script | <a href="vep_script.html">Documentation</a> | <a href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/variant_effect_predictor.tar.gz?view=tar&root=ensembl&pathrev=branch-ensembl-[[SPECIESDEFS::ENSEMBL_VERSION]]">Download latest version</a></li>
  <li> using Ensembl's perl API | <a href="/info/docs/api/variation/index.html">Documentation</a></li>
</ul>

<p>
The web version is suitable for users with small volumes of data or those who
prefer not to use command-line utilities. The script version is the most
flexible of the VEP, and allows users to process large volumes of data using
their own compute resources. The API is suitable for perl programmers looking to
incorporate features of the VEP into their own code.
</p>

<h2>Ensembl Variation</h2>

<p>For a comprehensive list of the consequence types used in Ensembl (including VEP results), 
have a look at our <a href="/info/docs/variation/data_description.html#classes">documentation</a>.  
Our online documentation also provides descriptions of <a href="/info/docs/variation/index.html">data and analyses in Ensembl variation</a>.
Read more about the VEP in <b>McClaren et. al.</b> (<a href="http://www.ncbi.nlm.nih.gov/pubmed/20562413">doi:10.1093/bioinformatics/btq330</a>).</p>
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</div><commit_msg>Added small changes to the text<commit_after><html>
<head>
<title>Variant Effect Predictor</title>
</head>
<body>

<div class="column-wrapper">
<h1>Variant Effect Predictor</h1>
</div>
<div class="column-wrapper">
  <div class="column-two">
    <div class="column-left">
      <div class="plain-box">
      <a href="/[[SPECIESDEFS::ENSEMBL_PRIMARY_SPECIES]]/UserData/UploadVariations" class="modal_link">
      <img src="/i/vep_logo_sm.png" title="Launch the online VEP!" alt="Variant Effect Predictor" /></a>

<p>
The VEP determines the effect of your variants (SNPs, insertions,
deletions, CNVs or structural variants) on genes, transcripts, and
protein sequence, as well as regulatory regions. Simply input the
coordinates of your variants and the nucleotide changes to find out the:</p>
<ul>
<li>genes affected by the variants</li>
<li>location of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions)</li>
<li>consequence your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift)</li>
<li>known variants that match yours, and the associated minor allele frequencies</li>
<li>SIFT and PolyPhen scores for changes protein sequence</li>
<li>... And more!</li>
</ul>
      <p class="center"><a
href="/[[SPECIESDEFS::ENSEMBL_PRIMARY_SPECIES]]/UserData/UploadVariations"
class="modal_link"><strong><i>Launch the online VEP tool!</i></strong></a></p>
<h2>Sample output</h2>
<p><img src="/i/help/vep_output.jpg" title="Sample VEP results table" alt="screenshot" /></p>

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  </div>
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    <div class="column-right" style="padding-left:2em">
<h2>How to access the Variant Effect Predictor</h2>
<p>
There are two ways to use the Variant Effect Predictor (VEP) for
predicting functional consequences of known and unknown variants:
</p>

<ul>
  <li>web interface | <a href="#web">Documentation</a> | <a
href="/[[SPECIESDEFS::ENSEMBL_PRIMARY_SPECIES]]/UserData/UploadVariations"
class="modal_link">Launch web interface</a></li>
  <li>standalone perl script | <a href="vep_script.html">Documentation</a> | <a href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/variant_effect_predictor.tar.gz?view=tar&root=ensembl&pathrev=branch-ensembl-[[SPECIESDEFS::ENSEMBL_VERSION]]">Download latest version</a> <!--</li>
  <li> using Ensembl's perl API | <a href="/info/docs/api/variation/index.html">Documentation</a></li>-->
</ul>

<p>
Use the web version if you have relatively small volumes of data or
prefer to avoid command-line scripts. The script version is more
flexible and allows processing of large volumes of data (it is written
using the Ensembl perl API, and can be incorporated into your own code
and extended).
</p>

<h2>Ensembl Variation</h2>
<p>For a comprehensive list of the consequence types used in Ensembl and the VEP, look at our <a href="/info/docs/variation/data_description.html#classes">documentation</a>.  
It also provides descriptions of the <a href="/info/docs/variation/index.html">data and analyses in Ensembl Variation</a>.
Read more about the VEP in <b>McLaren et. al.</b> (<a href="http://www.ncbi.nlm.nih.gov/pubmed/20562413">doi:10.1093/bioinformatics/btq330</a>).</p>
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