>First we need to make the VCF</p>
<div class="sourceCode" id="cb711"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb711-1"><a href="variant-annotation.html#cb711-1" tabindex="-1"></a><span class="kw">(</span><span class="ex">samtools</span><span class="kw">)</span> <span class="ex">[shas0113:</span> pearl-millet-play]--% samtools faidx resources/genome.fasta</span></code></pre></div>
<p>Then reheader the VCF parts:</p>
<div class="sourceCode" id="cb712"><pre class="sourceCode sh"><cod