eCode bash"><span id="cb4-1"><a href="#cb4-1"></a><span class="co"># index the reference. Output will be prefixed with "gtseq15_loci"</span></span>
<span id="cb4-2"><a href="#cb4-2"></a><span class="ex">/map/--%</span> bwa index -p gtseq15_loci -a is gtseq15_loci.fasta</span>
<span id="cb4-3"><a href="#cb4-3"></a></span>
<span id="cb4-4"><a href="#cb4-4"></a><span class="co"># here is what comes by on stdout </span></span>
<span id="cb4-5"><a href="#cb4-5"></a>[<span class="ex">bwa_index</span>] Pack FASTA.