Course_Materials/variant_calling/tutorial/040_example.html

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<h1 class="title"><a href="http://ngscourse.github.io/">NGS data analysis course</a></h1>
<h2 class="author"><strong>De novo mutations</strong></h2>
<h3 class="date"><em>(updated 21-10-2015)</em></h3>
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<h1 id="preliminaries">Preliminaries</h1>
<h2 id="software-used-in-this-practical">Software used in this practical:</h2>
<ul>
<li><a href="http://denovogear.sourceforge.net/" title="DeNovoGear">DeNovoGear</a> : A program to detect de novo variants using next-generation sequencing data.</li>
</ul>
<h2 id="file-formats-explored">File formats explored:</h2>
<ul>
<li>VCF Variant Call Format: see <a href="http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42">1000 Genomes</a> and <a href="http://en.wikipedia.org/wiki/Variant_Call_Format">Wikipedia</a> specifications.</li>
</ul>
<h1 id="exercise-4-identification-of-de-novo-mutations">Exercise 4: Identification of <em>de novo</em> mutations</h1>
<h2 id="discovery-of-de-novo-mutations">1. Discovery of <em>de novo</em> mutations</h2>
<p>When working with families we might be interested in identifying variants that appeared for the first time in one family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents or in the fertilised egg itself.</p>
<p>For this analysis we need to specify the family structure in a pedigree. The requested pedigree must be in [PED format] (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped).</p>
<pre><code>less trio.ped</code></pre>
<p>Run DeNovoGear:</p>
<pre><code>~/soft/denovogear/bin/denovogear dnm auto \
    --vcf trio.vcf \
    --ped trio.ped \
    --output_vcf trio_denovo.vcf</code></pre>
<h2 id="exercise">2. Exercise</h2>
<p>Open the BAM files corresponding to the 3 related individuals in IGV. Include also the original VCF and the VCF containing the <em>de novo</em> mutations.</p>
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