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<p><ahref="https://karchinlab.org/opencravat/installers/OpenCRAVAT.2.2.9.pkg">Mac OS installer</a></p>
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<p>Right-click the downloaded file and select “Open”. Your Mac may ask you to confirm stating that the file was not downloaded from the App Store. Click “Open” button. Just double-clicking the installer may not enable this “Open” option.</p>
<p>In MacOS, you can also launch OpenCRAVAT via clicking on the application in your Applications folder. In Windows, you can click the desktop Icon to launch it.</p>
<p>Before we move on, let’s take a look at the overall workflow for annotating in the GUI. We’ll start out by 1) submitting our input file, 2) selecting the annotators, and then 3) submitting our job.</p>
<p>Now that we’ve filtered, let’s go back to the Summary Tab:</p>
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<p><imgsrc="images/oc-visualize-tab.png" class="img-fluid"> In the Summary tab, we can see information about the annotated variants, such as from the sequence ontology. We can get the counts within a sequence ontology category by mousing over that category in our plot:</p>
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<p><imgsrc="images/oc-visualize-seq-ontology.png" class="img-fluid"> These visualizations can be moved around and pinned. Using the camera icon, you can also save these visualizations.</p>
Before we move on, let's take a look at the overall workflow for annotating in the GUI. We'll start out by 1) submitting our input file, 2) selecting the annotators, and then 3) submitting our job.
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@@ -240,7 +240,7 @@ When our job is finished, we can [view our results and filter them](#filter-resu
<spanid="cb10-6"><ahref="#cb10-6" aria-hidden="true" tabindex="-1"></a> query <spanclass="op">=</span><spanclass="ss">f'select score, nseq from sift where chrom="</span><spanclass="sc">{</span>chrom<spanclass="sc">}</span><spanclass="ss">" and pos=</span><spanclass="sc">{</span>pos<spanclass="sc">}</span><spanclass="ss"> and ref="</span><spanclass="sc">{</span>ref_base<spanclass="sc">}</span><spanclass="ss">" and alt="</span><spanclass="sc">{</span>alt_base<spanclass="sc">}</span><spanclass="ss">";'</span></span>
<spanid="cb10-8"><ahref="#cb10-8" aria-hidden="true" tabindex="-1"></a> result <spanclass="op">=</span><spanclass="va">self</span>.cursor.fetchone()</span>
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<spanid="cb10-9"><ahref="#cb10-9" aria-hidden="true" tabindex="-1"></a><spanclass="cf">if</span> result <spanclass="kw">is</span><spanclass="kw">not</span><spanclass="va">None</span>:</span>
<spanid="cb10-2"><ahref="#cb10-2" aria-hidden="true" tabindex="-1"></a><spanclass="kw">query</span><spanclass="op">=</span> f<spanclass="st">'select score, nseq from sift where chrom="{chrom}"'</span></span>
<spanid="cb11-6"><ahref="#cb11-6" aria-hidden="true" tabindex="-1"></a> query <spanclass="op">=</span><spanclass="ss">f'select score, nseq from sift where chrom="</span><spanclass="sc">{</span>chrom<spanclass="sc">}</span><spanclass="ss">" and pos=</span><spanclass="sc">{</span>pos<spanclass="sc">}</span><spanclass="ss"> and ref="</span><spanclass="sc">{</span>ref_base<spanclass="sc">}</span><spanclass="ss">" and alt="</span><spanclass="sc">{</span>alt_base<spanclass="sc">}</span><spanclass="ss">";'</span></span>
<spanid="cb11-8"><ahref="#cb11-8" aria-hidden="true" tabindex="-1"></a> result <spanclass="op">=</span><spanclass="va">self</span>.cursor.fetchone()</span>
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<spanid="cb11-9"><ahref="#cb11-9" aria-hidden="true" tabindex="-1"></a><spanclass="cf">if</span> result <spanclass="kw">is</span><spanclass="kw">not</span><spanclass="va">None</span>:</span>
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