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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">VCF tracks</h1></header><article><div><span><h1><a class="anchor" aria-hidden="true" id="variant-tracks-vcf"></a><a href="#variant-tracks-vcf" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Variant Tracks (VCF)</h1>
<p>Beginning in JBrowse 1.9.0, JBrowse can display feature data directly from VCF files, and has an <code>HTMLVariants</code> track type that is optimized for displaying the potentially large amounts of detailed data that go with each variant.</p>
<p><img src="/docs/assets/config/JBrowse_variant_details.png" alt="800px|center|thumb|Variant details display, showing a genotypes summary and sortable table of 1094 genotypes."></p>
<p>VCF files used with the <code>VCFTabix</code> must be compressed with <code>bgzip</code> and indexed with <code>tabix</code>, both of which are part of the <a href="http://samtools.sourceforge.net/">samtools</a> package. This is usually done with commands like:</p>
<pre><code class="hljs"> bgzip my<span class="hljs-selector-class">.vcf</span>
tabix -<span class="hljs-selector-tag">p</span> vcf my<span class="hljs-selector-class">.vcf</span><span class="hljs-selector-class">.gz</span>
</code></pre>
<h2><a class="anchor" aria-hidden="true" id="example-vcf-based-variant-track-configuration"></a><a href="#example-vcf-based-variant-track-configuration" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Example VCF-based Variant Track Configuration</h2>
<p>Here is an example track configuration stanza for a variant track displaying data directly from a <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41">VCF file</a>. Note that the URL in <code>urlTemplate</code> is relative to the directory where the configuration file is located. Note that <code>tbiUrlTemplate</code> can also be used if your tbi file is named anything other than the urlTemplate with .tbi added to the end.</p>
<pre><code class="hljs css languages- {.javascript}"> {
<span class="hljs-attr">"label"</span> : <span class="hljs-string">"mysnps"</span>,
<span class="hljs-attr">"key"</span> : <span class="hljs-string">"SNPs from VCF"</span>,
<span class="hljs-attr">"storeClass"</span> : <span class="hljs-string">"JBrowse/Store/SeqFeature/VCFTabix"</span>,
<span class="hljs-attr">"urlTemplate"</span> : <span class="hljs-string">"mydata.vcf.gz"</span>,
<span class="hljs-attr">"type"</span> : <span class="hljs-string">"JBrowse/View/Track/HTMLVariants"</span>
}
</code></pre>
<p>Alternatively, if you are using the tracks.conf format, then a similar example would look like the following</p>
<pre><code class="hljs">[ tracks.myvcf ]
storeClass = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate = mydata.vcf.gz
category = VCF
type = JBrowse/View/Track/CanvasVariants
key = SNPs from VCF
</code></pre>
<p>Note that the file mydata.vcf.gz is resolved relative to the "data directory" being used, so just put the file inside the same directory as the trackList.json or tracks.conf. You can also use relative URL or fully qualified HTTP(s) urls in the urlTemplate parameter too</p>
<p>Also note: the tabix index (".tbi"), CSI index (".csi"), or tribble index (".idx") must be available as well. The tabix index is the default and it will simply look for the urlTemplate parameter with ".tbi" added on the end if nothing else is specified. If you are using CSI index, then manually specify the csiUrlTemplate parameter.</p>
<h3><a class="anchor" aria-hidden="true" id="vcf-tribble"></a><a href="#vcf-tribble" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>VCF-Tribble</h3>
<p>JBrowse 1.14 added support for VCF tribble indexes from htsjdk. Users can open tracks that use VCF tribble using the "Track"->"Open track" option or specify it in their config manually using the storeClass <code>JBrowse/Store/SeqFeature/VCFTribble</code></p>
<h3><a class="anchor" aria-hidden="true" id="using-vcf-filters-in-configuration"></a><a href="#using-vcf-filters-in-configuration" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Using VCF Filters in configuration</h3>
<p>The two variables hideNotFilterPass or hideFilterPass can be used to define whether to filter some variants by default. For example adding hideNotFilterPass: 1 will show the variants that passed all filters by default (i.e. it hides all the features that didn't pass all the filters)</p>
<p><code>"hideNotFilterPass": 1</code></p>
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