update with requested fixes

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- <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Open Cravat Vignettes</span></span></a>
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@@ -251,7 +251,7 @@ <h2 data-number="5.1" class="anchored" data-anchor-id="why-filter"><span class="
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 <h2 data-number="5.2" class="anchored" data-anchor-id="filtering-roadmap"><span class="header-section-number">5.2</span> Filtering Roadmap</h2>
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@@ -305,7 +305,7 @@ <h3 data-number="5.4.2" class="anchored" data-anchor-id="samples"><span class="h
 <p>You can remove variants associated with a set of sample IDs by clicking on the checkboxes here. For example, we want all of the variants that are associated with the mother. We’ll click on the “mother” checkbox until it is a green check.</p>
 <p><img src="images/mother-filter1.png" class="img-fluid"> If we look at the Variant tab, we can see that our variants include multiple members:</p>
 <p><img src="images/mother-all-result.png" class="img-fluid"> Here’s a visual summary of the results.</p>
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 <p>To exclude samples, click on the checkbox until you see a red x.</p>
 <p><img src="images/mother-exclusive-filter.png" class="img-fluid"> After filtering, we find that 385 variants are exclusive to the mother. We can confirm this by going to the <strong>Variant</strong> tab:</p>
 <p><img src="images/mother-exclusive-result.png" class="img-fluid"> Here’s the visual summary:</p>
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 <p><img src="images/gene-filter.png" class="img-fluid"> Going to the <strong>Variant</strong> tab, we can confirm that the variants belong to BRCA1 and BRCA2.</p>
 <p><img src="images/gene-filter-result.png" class="img-fluid"> Here’s the visual summary of the filter:</p>
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 <p><img src="images/variant-filter2.png" class="img-fluid"> C. 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>
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 <p><img src="images/add-filter2.png" class="img-fluid"> If we look at the <strong>Variant</strong> tab, we can see that our combined filter selected both Pathogenic and Missense Variants.</p>
 <p><img src="images/add-filter-result.png" class="img-fluid"></p>
 <p>When we apply the filter, we get 9 variants that meet both criteria. Here’s a visual summary of the filtering:</p>
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 <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>
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 <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.</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>
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 <p>Let’s combine a sample filter with a grouped variant filter.</p>
 <p>In our case, we want variants that are associated with the mother of the family combined with our joint missense/pathogenic variant filter.</p>
 <p><img src="images/case-study-filter.png" class="img-fluid"></p>
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