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<article id="post-11201" class="post-11201 event_listing type-event_listing status-expired has-post-thumbnail hentry event_listing_category-ncbi-education event_listing_type-ncbi-codeathon">
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<header class="entry-header">
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<h1 class="entry-title">VCF Files for Population Genomics: Scaling to Millions of Samples</h1> </header><!-- .entry-header -->
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<div class="wpem-event-single-image"><link rel="image_src" href="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/04/vcf_codeathon.png"/><img data-recalc-dims="1" decoding="async" itemprop="image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/04/vcf_codeathon.png" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/04/vcf_codeathon.png?w=1108&ssl=1" alt="VCF Files for Population Genomics: Scaling to Millions of Samples" /></div>
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<div class="wpem-event-title">
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<h3 class="wpem-heading-text">VCF Files for Population Genomics: Scaling to Millions of Samples</h3>
|
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</div>
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<div class="wpem-viewed-event wpem-tooltip wpem-tooltip-bottom"><i class="wpem-icon-eye"></i> 21066 <span class="wpem-tooltiptext">21066 people viewed this event.</span>
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<!-- Event description section start-->
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<div class="wpem-single-event-body-content">
|
||
<h6>Codeathon Outcomes:</h6>
|
||
<p>This codeathon concluded on August 4th, 2023. To see what teams accomplished, check out their <a class="c-link" href="https://github.com/search?q=topic%3Avcf-4-population-genomics+org%3ANCBI-Codeathons+fork%3Atrue&type=repositories" target="_blank" rel="noopener noreferrer" data-stringify-link="https://github.com/search?q=topic%3Avcf-4-population-genomics+org%3ANCBI-Codeathons+fork%3Atrue&type=repositories" data-sk="tooltip_parent">GitHub repositories</a> and/or watch the <a class="c-link" href="https://www.nlm.nih.gov/oet/ed/ncbi/8-4_codeathon.html" target="_blank" rel="noopener noreferrer" data-stringify-link="https://www.nlm.nih.gov/oet/ed/ncbi/8-4_codeathon.html" data-sk="tooltip_parent">recorded final presentations</a><a href="https://github.com/search?q=topic%3Avcf-4-population-genomics+org%3ANCBI-Codeathons+fork%3Atrue&type=repositories">.</a></p>
|
||
<h6>Codeathon Description:</h6>
|
||
<p><span data-contrast="auto">NCBI and NIAID co-hosted a codeathon, </span><b><i><span data-contrast="auto">VCF Files for Population Genomics: Scaling to Millions of Samples, </span></i></b><span data-contrast="auto">held virtually from July 31</span><span data-contrast="auto">st</span><span data-contrast="auto"> to August 4</span><span data-contrast="auto">th</span><span data-contrast="auto">, 2023</span><b><i><span data-contrast="auto">.</span></i></b><span data-contrast="auto"> VCF, or Variant Call Format Files, are a widely used file for storing information about genetic variations across multiple samples. This event aimed to bring together experts in viral evolution, molecular epidemiology, and population genomics to explore methods for computing on the scale of millions of records using VCF files as inputs, with </span><a href="https://aws.amazon.com/marketplace/pp/prodview-imrj2amkaekae?sr=0-7&ref_=beagle&applicationId=AWSMPContessa"><span data-contrast="none">SARS-CoV-2 VCFs</span></a><span data-contrast="auto"> serving as a case study.</span><span data-ccp-props="{"201341983":0,"335559739":160,"335559740":259}"> </span></p>
|
||
<p><span data-contrast="auto">We invited both programmers and non-programming subject matter experts to apply for this event. During the week-long codeathon, teams of 5-8 people collaborated virtually to design visualizations and write software to address the following objectives:</span><span data-ccp-props="{"201341983":0,"335559739":160,"335559740":259}"> </span></p>
|
||
<ul>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props="{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" data-aria-posinset="1" data-aria-level="1"><span data-contrast="auto">Explore the use of </span><a href="https://www.ncbi.nlm.nih.gov/sra/docs/sars-cov-2-variant-calling/"><span data-contrast="none">SARS-CoV-2 variant call format (VCF) files</span></a><span data-contrast="auto"> as input to downstream applications such as viral classification, characterization, and phylogenetic tree construction.</span><span data-ccp-props="{"201341983":0,"335559739":160,"335559740":259}"> </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props="{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" data-aria-posinset="2" data-aria-level="1"><span data-contrast="auto">Estimate intra-host sequence diversity and predict emerging new variants of SARS-CoV-2 using VCFs as input.</span><span data-ccp-props="{"201341983":0,"335559739":160,"335559740":259}"> </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props="{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" data-aria-posinset="2" data-aria-level="1"><span data-contrast="auto">Streamline processes to assess the current therapeutic and preventative options using VCFs. For example, assessing genome-scale responses to vaccines or therapeutics. </span><span data-ccp-props="{"201341983":0,"335559739":160,"335559740":259}"> </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props="{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}" data-aria-posinset="2" data-aria-level="1"><span data-contrast="auto">Enhance and facilitate the data clustering process and modeling for predictions using VCFs.</span><span data-ccp-props="{"201341983":0,"335559739":160,"335559740":259}"> </span></li>
|
||
</ul>
|
||
<p><span data-contrast="auto">The codeathon was designed to be cooperative rather than competitive, and teams shared ideas and technical expertise. </span></p>
|
||
<p><span data-contrast="auto"><a href="https://github.com/NCBI-Codeathons?q=vcf-4&type=all">Team products</a> are publicly available through the NCBI Codeathons GitHub Organization.</span></p>
|
||
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||
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<h3 class="wpem-heading-text">Date And Time</h3>
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||
07-31-2023 @ 12:00 PM (EST) </span>
|
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to <br />
|
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<span class="wpem-event-date-time-text">08-04-2023 @ 03:00 PM (EST) </span>
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06-17-2023 <!-- Registration End Date End-->
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Online event </div>
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