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type="text/javascript"> /* <![CDATA[ */ (function() { var dropdown = document.getElementById( "archives-dropdown-2" ); function onSelectChange() { if ( dropdown.options[ dropdown.selectedIndex ].value !== '' ) { document.location.href = this.options[ this.selectedIndex ].value; } } dropdown.onchange = onSelectChange; })(); /* ]]> */ </script> </aside> <aside id="meta-2" class="widget widget_meta"> <h3 class='widget-title'>Meta</h3> <ul> <li><a href="https://www.ensembl.info/wp-login.php">Log in</a></li> <li><a href="https://www.ensembl.info/feed/">Entries feed</a></li> <li><a href="https://www.ensembl.info/comments/feed/">Comments feed</a></li> <li><a href="https://en-gb.wordpress.org/">WordPress.org</a></li> </ul> </aside> <aside id="custom_html-3" class="widget_text widget widget_custom_html"> <div class="textwidget custom-html-widget">© 2018 EMBL-EBI. All rights reserved. Background image by Spencer Phillips</div> </aside> <aside id="eu_cookie_law_widget-2" class="widget widget_eu_cookie_law_widget"> <div class="hide-on-button" data-hide-timeout="30" data-consent-expiration="365" id="eu-cookie-law" > <form method="post"> <input type="submit" value="Close and accept" class="accept" /> </form> This website requires cookies, and the limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our <a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice" rel=""> Privacy Policy </a> </div> </aside> </div> </div> </div> <div id="primary" class="content-area col-lg-9" itemprop="mainContentOfPage"> <div id="content" class="site-content" role="main" itemscope itemtype="http://schema.org/Article"> <article id="post-15240" class="post-15240 post type-post status-publish format-standard hentry category-02-ensembl-vep tag-custom-annotation tag-vep"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Cool stuff the Ensembl VEP can do: new options for custom annotation</h1> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/01/26/cool-stuff-the-ensembl-vep-can-do-new-options-for-custom-annotation/" rel="bookmark"><time class="entry-date published" datetime="2024-01-26T13:32:22+00:00" itemprop="datepublished">26th January 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/bmoore/" rel="author" itemprop="url"><span itemprop="name">Ben (Outreach)</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Cool stuff the Ensembl VEP can do: new options for custom annotation</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>During the latest Ensembl VEP releases, we have been enhancing the options available to you when you annotate variants against your own reference data as ‘custom annotation’. Here we detail some of those improvements.</p> <span id="more-15240"></span> <p>The ‘–custom’ option enables you to integrate genomics data in standard file formats (VCF, GTF,GFF3, BED, bigWig) into Ensembl VEP analysis. All the information on using custom annotations with Ensembl VEP is available in our <a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html" target="_blank" rel="noreferrer noopener">public documentation</a>. Check the <a href="http://ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options" target="_blank" rel="noreferrer noopener">Options section</a> for a list of all available options, including those mentioned below.</p> <h1 class="wp-block-heading">Named options in custom annotation argument</h1> <p>Since Ensembl VEP 110, each custom annotation source can be configured using a comma-separated list of key-value pairs:</p> <p><strong>./vep</strong> […] –custom file=<strong>Filename</strong>,short_name=<strong>Short_name</strong>,format=<strong>File_type</strong>,<strong>type</strong>=<strong>Annotation_type</strong>,fields=<strong>VCF_fields</strong></p> <p>These named options in the custom annotation argument improve readability and are easier to use as you don’t need to remember the order they need to be in.</p> <p>For backwards compatibility, Ensembl VEP still supports the positional options from previous versions, as detailed in our <a href="http://ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options" target="_blank" rel="noreferrer noopener">public documentation</a>. However, note that the new features presented here can only be enabled using the named options feature.</p> <h1 class="wp-block-heading">Overlap configuration </h1> <p>You can now configure which reference features are returned by specifying the kind of overlaps you wish to see.</p> <p>You can select different match types (<a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html#opt_type" target="_blank" rel="noreferrer noopener"><strong>type</strong></a>):</p> <ul> <li><strong>overlap</strong><strong> (default):</strong> report annotations that overlap the variant by even 1 base pair.</li> <li><strong>exact</strong><strong>:</strong> report annotations whose coordinates match exactly those of the variant.</li> <li><strong>within</strong><strong> (new):</strong> report annotations within the variant.</li> <li><strong>surrounding</strong><strong> (new):</strong> report annotations that completely surround the variant.</li> </ul> <p>and different distances or % overlap:</p> <ul> <li><a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html#opt_overlap_cutoff" target="_blank" rel="noreferrer noopener"><strong>overlap_cutoff</strong></a><strong>: </strong>minimum percentage overlap between annotation and variant.</li> <li><a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html#opt_reciprocal" target="_blank" rel="noreferrer noopener"><strong>reciprocal</strong></a><strong>: </strong>mode of calculating the overlap percentage for <strong>overlap_cutoff</strong>. <ul> <li><strong>0</strong>: percentage of annotation covered by the variant.</li> <li><strong>1</strong>: percentage of the variant covered by annotation.</li> </ul> </li> <li><a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html#opt_distance" target="_blank" rel="noreferrer noopener"><strong>distance</strong></a><strong>: </strong>distance (in base pairs) to the ends of the overlapping feature.</li> </ul> <p>Additional match configuration is available when you are using custom VCF: </p> <ul> <li><a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html#opt_same_type" target="_blank" rel="noreferrer noopener"><strong>same_type</strong></a><strong>: </strong>only match identical variant classes (for instance, only match deletion variant with deletion annotations).</li> </ul> <h1 class="wp-block-heading">Summary statistics for custom annotations</h1> <p>Ensembl VEP now is also able to calculate summary statistics (mean, minimum, maximum, count and sum) for custom annotations based on the scores of the different file formats with the <a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html#opt_summary_stats" target="_blank" rel="noreferrer noopener"><strong>summary_stats</strong></a><strong> </strong>option. By default, no statistics are calculated.</p> <p>The scores are obtained differently depending on the custom file format in use:</p> <ul> <li>For BED, GTF and GFF files, the score is retrieved from the score column (<a href="https://www.ensembl.org/info/website/upload/bed.html" target="_blank" rel="noreferrer noopener">5th column in BED files</a> and <a href="https://www.ensembl.org/info/website/upload/gff.html" target="_blank" rel="noreferrer noopener">6th column in GTF/GFF</a>).</li> <li>For BigWig files, the score is retrieved from the <a href="https://www.ensembl.org/info/website/upload/wig.html#datavalues" target="_blank" rel="noreferrer noopener">data values</a>.</li> <li>For VCF files, the score is retrieved from the <a href="http://samtools.github.io/hts-specs/" target="_blank" rel="noreferrer noopener">quality (QUAL) column</a>.</li> </ul> <h1 class="wp-block-heading">Number of matching records to display</h1> <p>When using large structural variants with custom annotation (specially BED/BigWig files), we may get more matching records than desired, creating heavy files that are hard to parse and handle. As such, Ensembl VEP now only reports 50 matching records by default. Any remaining records are represented with an ellipsis (<strong>…</strong>).</p> <p>To change this behaviour, please use the new option <a href="https://ensembl.org/info/docs/tools/vep/script/vep_custom.html#opt_num_records" target="_blank" rel="noreferrer noopener"><strong>num_records</strong></a>:</p> <ul> <li>Select any positive value to display that specific number of records.</li> <li>Use <strong>all</strong> to display every single matching record. Note that this may create really large files that are computationally intensive to process.</li> <li>Use <strong>0</strong> to display uniquely an ellipsis (<strong>…</strong>) if there are matching records.</li> </ul> <p>If you have comments on the new features or ideas on how to improve them, please contact us on the <a href="https://www.ensembl.org/Help/Contact" target="_blank" rel="noreferrer noopener">Ensembl Helpdesk</a>.</p> </div> <div class="tags-links"><a href="https://www.ensembl.info/tag/custom-annotation/" rel="tag">custom annotation</a> <a href="https://www.ensembl.info/tag/vep/" rel="tag">VEP</a></div></article> <nav class="navigation post-navigation" aria-label="Posts"> <h2 class="screen-reader-text">Post navigation</h2> <div class="nav-links"><div class="nav-previous"><a href="https://www.ensembl.info/2024/01/18/downtime-of-the-ensembl-search-and-asia-mirror/" rel="prev"><span class="meta-nav" aria-hidden="true">Previous</span> <span class="screen-reader-text">Previous post:</span> <span class="post-title">Downtime of Ensembl search</span></a></div><div class="nav-next"><a href="https://www.ensembl.info/2024/02/02/getting-to-know-us-bilal-from-ensembl-applications/" rel="next"><span class="meta-nav" aria-hidden="true">Next</span> <span class="screen-reader-text">Next post:</span> <span class="post-title">Getting to know us: Bilal from Ensembl Applications</span></a></div></div> </nav> </div> <footer class="site-info" itemscope itemtype="http://schema.org/WPFooter"> <a href="http://wordpress.org/" title="Semantic Personal Publishing Platform">Proudly powered by WordPress</a>. 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