overview.html

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        Non-human primates, such as Rhesus macaques, are a powerful genetic model of human disease.  mGAP seeks to fill several major voids to promote genomic analyses and the study of human genetic disease in this key pre-clinical model.
        The database provides open access to rhesus macaque genomic and phenotypic data, with data primarily generated using subjects from <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-externalData.view">the National Primate Research Center system and other captive NHP colonies.</a>.
        <br><br>
        <span style="font-weight: bold">NEW: Click the video icon (<i class="fa-solid fa-video mgap-video-icon" data-video="overview" data-video-title="mGAP Overview"></i>) to load an overview video describing mGAP's features. There are additional icons/videos below, or <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-tutorials.view">view our tutorials page</a> for more detail.</span>
        <br>
        <h4><span style="text-decoration: underline">Short Variant Catalog:</span> <img style="vertical-align: sub" width="40px" src="<%=contextPath%>/mgap/images/SNV.png" alt="SNV"></h4>
        The primary dataset generated by mGAP is a catalog of short variants (summarized to the right). Raw sequence data are <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-dataProcessing.view">analyzed using a vetted pipeline</a> designed to produce high-confidence genotype calls.
        The resulting variants are <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-annotation.view">annotated using a wide range of data sources</a>, including predicted function, overlap with regulatory elements and association with phenotypes and diseases.
        <br>
        <ul style="padding-top: 10px;">
            <li>Use the <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?">Genome Browser</a> to view and search data. <i class="fa-solid fa-video mgap-video-icon" data-video="genome-browser" data-video-title="Genome Browser Overview"></i></li>
            <li class="mgap-lucene-link" hidden="hidden">Use our new <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?target=variantSearch">Full-text Search</a> tool to query variants based on gene, or using our <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-annotation.view">extensive annotations</a> <i class="fa-solid fa-video mgap-video-icon" data-video="variant-search" data-video-title="Variant Full-text Search (BETA)"></i></li>
            <li>View our list of <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-variantList.view">Predicted Damaging Variants</a>, which is a list of predicted high-impact or disease associated variants, generated from each release <i class="fa-solid fa-video mgap-video-icon" data-video="predicted-damaging-variants" data-video-title="Predicted Damaging Variants"></i></li>
            <li>Unlike many datasets, mGAP has genotype-level data, <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=clinical">often connected to living animals from pedigreed breeding colonies</a></li>
            <li>Download raw data, including <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=datasets">sequence data</a> and <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=variants">variant data</a></li>
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        <h4><span style="text-decoration: underline;">Structural Variant Catalog:</span> <img style="vertical-align: sub" width="40px" src="<%=contextPath%>/mgap/images/SV.png" alt="SV"></h4>
        We have released a draft dataset with structural variants generated from PacBio sequencing of 44 Rhesus macaques. These data complement the short variant catalog by detecting categories of variants not readily accomplished with short read Illumina data.
        <br>
        <ul style="padding-top: 10px;">
            <li>Use the <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?nhpSpecies=Rhesus macaque&activeTracks=mGAP Structural Variants 1.0&location=11:6,936,982..7,002,783">Genome Browser</a> to view and search structural variant data</li>
        </ul>

        <h4><span style="text-decoration: underline;">NHP Models of Human Disease:</span> <img style="vertical-align: sub" width="40px" src="<%=contextPath%>/mgap/images/phenotypes.png" alt="Phenotypes"></h4>
        NHPs serve as essential pre-clinical models for a range of human diseases. The mGAP site supports this work by providing information about published NHP disease/phenotype models, and by providing summaries of the annotated variant catalog to help identify novel disease-associated variants.
        <br>
        <ul style="padding-top: 10px;">
            <li>Tutorial on searching phenotypes and variants <i class="fa-solid fa-video mgap-video-icon" data-video="phenotypes-and-models" data-video-title="Phenotypes and Models"></i></li>
            <li>View our list of <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=model">Published NHP Disease Models</a></li>
            <li>View the list of <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-phenotypeList.view">Genes and OMIM diseases/phenotypes</a> where predicted damaging variants were detected</li>
            <li>View our list of <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-variantList.view">Predicted Damaging Variants</a>, which is a list of predicted high-impact or disease associated variants, generated from each release</li>
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        <h4 style="font-style: italic;margin-top: 0;">Summary of Current Release:</h4>
        <br>
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        <h5 style="font-style: italic;">Breakdown of Coding Potential:</h5>
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        <div style="font-style: italic;padding-top:10px;">**Coding potential defined using <a href="http://snpeff.sourceforge.net/SnpEff_manual.version_4_0.html">SnpEff</a></div>

        <h5 style="font-style: italic;">Breakdown By Variant Type:</h5>
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        <h5 style="font-style: italic;">Summary of Annotations:</h5>
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