ld-i-prepare-my-data" class="anchor"></a>How, specifically, should I prepare my data?</h2>
<p>The starting point for <code>microhaplot</code> requires:</p>
<ol style="list-style-type: decimal">
<li>An indexed, SAM file of reads aligned to the reference sequences for each amplicon.</li>
<li>A VCF file whose contents define the positions in each reference sequence from which you want to extract variants into microhaplotypes. Note that the <em>individuals</em> that appear in the VCF file need not be the same o