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laderast committed Aug 9, 2024
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.55">
<meta name="generator" content="quarto-1.5.45">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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</head>

<body class="fullcontent">
<body>

<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">

<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<div class="quarto-alternate-formats"><h2>Other Formats</h2><ul><li><a href="filtering.rst"><i class="bi bi-file"></i>reST</a></li></ul></div></div>
<main class="content" id="quarto-document-content">

<header id="title-block-header" class="quarto-title-block default">
Expand Down Expand Up @@ -77,10 +78,13 @@ <h1>Filtering Roadmap</h1>
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">A["Results Viewer"] --&gt; B
B["Build Filter in GUI"] --&gt; C["Save JSON filter"]
C --&gt; D["Apply filter to New Set"]
C --&gt; E["Apply Filter on CLI"]
<pre class="mermaid mermaid-js">flowchart TD
A["Results Viewer"] --&gt; B
B["Build Filter in GUI"]
B --&gt; F["Explore Filtered Data"]
F --&gt; G["Save JSON filter"]
G --&gt; D["Apply filter to New Set"]
G --&gt; E["Apply Filter on CLI"]
</pre>
</div>
<p></p></figure><p></p>
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<section id="samples" class="level2">
<h2 class="anchored" data-anchor-id="samples">Samples</h2>
<p>You can remove variants associated with a set of sample IDs by unselecting them in the checkboxes here.</p>
<div class="cell" data-layout-align="default">
<div class="cell-output-display">
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">graph TD
A["All Variants\n(n=1,738)"] --"Sample:mother"--&gt; B
B["Mother Variants\n(n=385)"]
</pre>
</div>
<p></p></figure><p></p>
</div>
</div>
</div>
<p>For example, we can filter for</p>
</section>
<section id="genes" class="level2">
<h2 class="anchored" data-anchor-id="genes">Genes</h2>
<p>Gene-level filtering can be done here. You can dinput a list of genes, separated by line-breaks</p>
<p>Gene-level filtering can be done here. You can input a list of genes, separated by line-breaks</p>
<div class="cell" data-layout-align="default">
<div class="cell-output-display">
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">graph TD
A["All Variants\n(n=1,738)"] --"Gene:(BRCA1,BRCA2)"--&gt; B
B["BRCA1/BRCA2 Genes\n(n=63)"]
</pre>
</div>
<p></p></figure><p></p>
</div>
</div>
</div>
</section>
<section id="sample-properties" class="level2">
<h2 class="anchored" data-anchor-id="sample-properties">Sample Properties</h2>
</section>
<section id="variant-properties" class="level2">
<h2 class="anchored" data-anchor-id="variant-properties">Variant Properties</h2>
<p>In variant properties, you can filter by variant type based on your annotations. For example, let’s filter to missense variants.</p>
<p>Under Variant Filter:</p>
<ol type="1">
<li>Click on “Query Builder”.</li>
<li>Mouse into the left bottom corner of the query builder window, and click the “+” sign.</li>
</ol>
<p><img src="images/variant-filter.png" class="img-fluid"></p>
<p>Make your filter by selecting the following dropdown boxes:</p>
<ol type="1">
<li>Variant Annotation</li>
<li>Sequence Ontology</li>
<li>One of</li>
<li>Missense checkbox</li>
</ol>
<p><img src="images/variant-filter2.png" class="img-fluid"> Finally, click the “Apply Filter” Button:</p>
<p><img src="images/variant-apply-filter.png" class="img-fluid"></p>
<p>You will be left with 299 variants. Here’s a visual summary of what we did:</p>
<div class="cell" data-layout-align="default">
<div class="cell-output-display">
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">graph TD
A["All Variants\n(n=1,738)"] --"Sequence Ontology:\nMissense"--&gt; B["Missense Variants\n(n=299)"]

</pre>
</div>
<p></p></figure><p></p>
</div>
</div>
</div>
</section>
</section>
<section id="boolean-operations" class="level1">
<h1>Boolean Operations</h1>
<p>You can build more sophisticated operations by combining each filter step using Boolean logic.</p>
<p>For example, we might want variants that …</p>
<section id="and-logic" class="level2">
<h2 class="anchored" data-anchor-id="and-logic">AND logic</h2>
<p>By default, the filters are combined using <strong>AND</strong> logic, which are more restrictive, because they require variants to meet both filters.</p>
<p>Here’s an example of using <strong>AND</strong> logic. Here we are combining two filters: Missense Variants (from Variant Annotation –&gt; Sequence Ontology) and Pathogenic variants (from ClinVar –&gt; Clinical Significance).</p>
<p><img src="images/and-filter.png" class="img-fluid"> When we apply the filter, we get 9 variants that meet both criteria. Here’s a visual summary of the filtering:</p>
<div class="cell" data-layout-align="default">
<div class="cell-output-display">
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">graph TD
A["All Variants\n(n=1,738)"] --"Sequence Ontology:\nmissense"--&gt; B["Missense Variants\(n=299)"]
A --"Clinical Significance:\nPathogenic"--&gt; C["Pathogenic Variants\n(n=10)"]
B --"AND"--&gt; E["Pathogenic AND Missense\n(n=9)"]
C --"AND"--&gt; E
</pre>
</div>
<p></p></figure><p></p>
</div>
</div>
</div>
</section>
<section id="or-logic" class="level2">
<h2 class="anchored" data-anchor-id="or-logic">OR Logic</h2>
<p>These filters can also be combined using <strong>OR</strong> logic, which is more permissive (that is, these filters will return a greater number than the <strong>AND</strong> logic) we might want variants that are either missense <strong>OR</strong> pathogenic.</p>
<p>We can do this by clicking the “and” that links our two filters, which will switch it to an “or”:</p>
<p><img src="images/or-filter.png" class="img-fluid"> When we apply the filter, we get 300 variants. The breakdown is below.</p>
<div class="cell" data-layout-align="default">
<div class="cell-output-display">
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">graph TD
A["All Variants\n(n=1,738)"] --"Sequence Ontology:\nmissense"--&gt; B["Missense Variants\n(n=299)"]
A --"Clinical Significance:\nPathogenic"--&gt; C["Pathogenic Variants\n(n=10)"]
B --"OR"--&gt; E["Pathogenic OR Missense\n(n=300)"]
C --"OR"--&gt; E
</pre>
</div>
<p></p></figure><p></p>
</div>
</div>
</div>
</section>
<section id="combining-and-or-logic" class="level2">
<h2 class="anchored" data-anchor-id="combining-and-or-logic">Combining AND / OR logic</h2>
<p>By default, when you click the “and” / “or” of one set of filters, all filters will be changed. If you want to combine <strong>AND</strong> / <strong>OR</strong> logic, you can group one of the logic operations using parentheses.</p>
<p>For example, say we want the above <strong>OR</strong> subset combined as an <strong>AND</strong> with those variants that have PS1 evidence. We can</p>
<p>This is what our final filter looks like:</p>
<p><img src="images/and-or-filter.png" class="img-fluid"> Here’s a visual breakdown of this complex filter:</p>
<div class="cell" data-layout-align="default">
<div class="cell-output-display">
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">graph TD
A["All Variants\n(n=1,738)"]--"Sequence Ontology:\nmissense"--&gt; B
A --"Clinical Significance:\nPathogenic"--&gt; C
subgraph OR
B["Missense Variants\n(n=299)"]
C["Pathogenic Variants\n(n=10)"]
B --"OR"--&gt; E["Pathogenic OR Missense\n(n=300)"]
C --"OR"--&gt; E
end
subgraph PS1
F["PS1 Variants\n(n=27)"]
end
E --"AND"--&gt; G["PS1 Variants AND\n(Missense OR Pathogenic)\n(n=27)"]
A --"ClinVar ACMG\nPS1 variants"--&gt; F
F --"AND"--&gt; G

</pre>
</div>
<p></p></figure><p></p>
</div>
</div>
</div>
</section>
<section id="not-logic" class="level2">
<h2 class="anchored" data-anchor-id="not-logic">NOT Logic</h2>
</section>
<section id="deleting-a-filter" class="level2">
<h2 class="anchored" data-anchor-id="deleting-a-filter">Deleting a Filter</h2>
</section>
<section id="case-study-filtering-pathogenic-variants" class="level2">
<h2 class="anchored" data-anchor-id="case-study-filtering-pathogenic-variants">Case Study: Filtering Pathogenic Variants</h2>
<div class="cell" data-layout-align="default">
<div class="cell-output-display">
<div>
<p></p><figure class="figure"><p></p>
<div>
<pre class="mermaid mermaid-js">graph TD
A["All Variants\n(n=1,738)"] --"PS1 ID\nhas data"--&gt; B
B["PS1 variants\n(n=36)"]
</pre>
</div>
<p></p></figure><p></p>
</div>
</div>
</div>
</section>
</section>
<section id="exporting-filters-as-json" class="level1">
<h1>Exporting Filters as JSON</h1>
<p>Filters can be exported and saved as JSON files for further reuse. They can be applied to a new set of variants in the GUI, or can be applied to result SQLite files on the command line.</p>
</section>
<section id="exporting-filters" class="level1">
<h1>Exporting Filters</h1>
<section id="applying-json-filters-in-the-gui" class="level1">
<h1>Applying JSON filters in the GUI</h1>
</section>
<section id="applying-filters-on-the-command-line" class="level1">
<h1>Applying filters on the command line</h1>
<section id="applying-json-filters-on-the-command-line" class="level1">
<h1>Applying JSON filters on the command line</h1>
<p>JSON filters can also be applied on the command-line using the <code>oc util filtersqlite</code> command. <a href="https://open-cravat.readthedocs.io/en/latest/Filter-And-Merge-SQLite.html">More information is here</a>.</p>
</section>

</main>
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