 href="#cb4-20"></a></span>
<span id="cb4-21"><a href="#cb4-21"></a><span class="co"># convert the SAMs to BAMs </span></span>
<span id="cb4-22"><a href="#cb4-22"></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> view -bhS satro_flashed_s<span class="va">${i}</span>_aln.sam <span class="op">&gt;</span> satro_flashed_s<span class="va">${i}</span>.bam<span class="kw">;</span> <span class="kw">done