n class="kw">;</span> <span class="kw">done</span></span>
<span id="cb4-27"><a href="#cb4-27"></a></span>
<span id="cb4-28"><a href="#cb4-28"></a></span>
<span id="cb4-29"><a href="#cb4-29"></a><span class="co"># Index the BAMs</span></span>
<span id="cb4-30"><a href="#cb4-30"></a><span class="ex">/map/--%</span> for i in <span class="dt">{1..384}</span><span class="kw">;</span> <span class="kw">do</span> <span class="ex">samtools</span> index satro_flashed_s<span class="va">${i}</span>_sorted.bam<span clas