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Geert van Geest committed Oct 18, 2023
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2 changes: 2 additions & 0 deletions 2023.9/day1/alignment/index.html
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Expand Up @@ -761,6 +761,8 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
<li>Generate and interpret the alignment statistics from <code>samtools flagstat</code></li>
</ul>
<h2 id="material">Material</h2>
<iframe width="560" height="315" src="https://www.youtube.com/embed/VhJ2JKE4fBs?si=dZWZ5A0lnMPIORtE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>

<p><a class="md-button" href="../../assets/pdf/04_sequencing_alignment.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
<h2 id="exercises">Exercises</h2>
<div class="admonition tip">
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Expand Up @@ -660,6 +660,7 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
<li>Explain what haplotypes are and how they can capture more genetic information compared to single small variants</li>
</ul>
<h2 id="material">Material</h2>
<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?si=Jfv_6TnErbWQBNGw&amp;list=PLoCxWrRWjqB3syM9-pdUSIClc2QkVMmH1" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
<p><strong>Course introduction:</strong></p>
<p><a class="md-button" href="../../assets/pdf/01_introduction.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
<p><strong>Introduction to variant analysis:</strong></p>
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Expand Up @@ -674,6 +674,8 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
<li>Explain how variant annotation can be added to a <code>vcf</code> file</li>
</ul>
<h2 id="material">Material</h2>
<iframe width="560" height="315" src="https://www.youtube.com/embed/DxuQ63jFMtM?si=SvQ5mVKjlIIS6A6h" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>

<p><a class="md-button" href="../../assets/pdf/07_variant_annotation.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
<h2 id="exercises">Exercises</h2>
<p>To use the human genome as a reference, we have downloaded the database with:</p>
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Expand Up @@ -779,6 +779,8 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
<li>Perform concordance between called variants and a truth set and evaluate performance of a variant calling workflow</li>
</ul>
<h2 id="material">Material</h2>
<iframe width="560" height="315" src="https://www.youtube.com/embed/8oiQOg40_co?si=bCnSYkIrWB_yCjjN" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>

<p><a class="md-button" href="../../assets/pdf/06_filtering_evaluation.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
<h2 id="exercises">Exercises</h2>
<h3 id="1-hard-filtering">1. Hard filtering</h3>
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Expand Up @@ -711,6 +711,8 @@ <h2 id="learning-outcomes">Learning outcomes</h2>
<li>Applying Base Quality Score Recalibration on an alignment file</li>
</ul>
<h2 id="material">Material</h2>
<iframe width="560" height="315" src="https://www.youtube.com/embed/5lwbusTbxHM?si=I_wt8MPKqSoWhGR5" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>

<p><a class="md-button" href="../../assets/pdf/05_variant_calling.pdf"><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><!--! Font Awesome Free 6.2.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2022 Fonticons, Inc.--><path d="M64 0C28.7 0 0 28.7 0 64v384c0 35.3 28.7 64 64 64h256c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zm192 0v128h128L256 0zM64 224h24c30.9 0 56 25.1 56 56s-25.1 56-56 56h-8v32c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16zm24 80c13.3 0 24-10.7 24-24s-10.7-24-24-24h-8v48h8zm72-64c0-8.8 7.2-16 16-16h24c26.5 0 48 21.5 48 48v64c0 26.5-21.5 48-48 48h-24c-8.8 0-16-7.2-16-16V240zm32 112h8c8.8 0 16-7.2 16-16v-64c0-8.8-7.2-16-16-16h-8v96zm96-128h48c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v32h32c8.8 0 16 7.2 16 16s-7.2 16-16 16h-32v48c0 8.8-7.2 16-16 16s-16-7.2-16-16V240c0-8.8 7.2-16 16-16z"/></svg></span> Download the presentation</a></p>
<p><a href="https://samtools.github.io/hts-specs/VCFv4.1.pdf">VCF format description</a></p>
<p><a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-">GATK best practices germline short variant workflow</a>:</p>
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