seq17_idx/s<span class="va">${i}</span>_idxstats.txt<span class="kw">;</span> <span class="kw">done</span></span></code></pre></div>
</div>
<div id="variant-detection" class="section level3">
<h3 class="hasAnchor">
<a href="#variant-detection" class="anchor"></a>Variant detection</h3>
<p>We are now set up to detect variants using freebayes. We show how we do that here, but emphasize that if you have already chosen a set of variants that form your microhaplotypes, you could just specify those with a pre-exis