ting what it is <strong>not</strong>.</p>
<ul>
<li>
<code>microhaplot</code> <strong>is not a SNP-caller or variant detector</strong>. It is not its job to determine if a variant might exist in a particular location or not. We assume you already know what variant position you want to look for by supplying <code>microhaplot</code> a variant caller file (VCF). <code>microhaplot</code> just extracts the bases sequenced on different reads at those positions.</li>
<li>
<code>microhaplot</code> <strong>is not an 