ting VCF file. You <em>don’t</em> need to do new variant detection if you don’t want to. (Of course, if it doesn’t take too long, you may as well do variant detection with every individual you have sequenced at the amplicons, so as to get as many variants as possible.)</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1"></a><span class="co"># index fasta reference file</span></span>
<span id="cb5-2"><a href="#cb5-2"></a><span 