"-1"></a><span class="fu">mkdir</span> results/vcf</span>
<span id="cb713-2"><a href="variant-annotation.html#cb713-2" tabindex="-1"></a><span class="ex">bcftools</span> concat results/vcf_parts/<span class="pp">*</span>.vcf.gz <span class="op">&gt;</span> results/vcf/all.vcf.gz</span></code></pre></div>
<p>Then run snpEff</p>
<div class="sourceCode" id="cb714"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb714-1"><a href="variant-annotation.html#cb714-1" tabindex="-1"></a> <span class