/snpEff.config</span></code></pre></div>
<p><strong>Step 2: Get the fasta and the GFF</strong><br />
We can download these directly to a folder and rename them sequences.fa and
genes.gff.gz</p>
<div class="sourceCode" id="cb709"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb709-1"><a href="variant-annotation.html#cb709-1" tabindex="-1"></a><span class="co"># make a directory to put them in</span></span>
<span id="cb709-2"><a href="variant-annotation.html#cb709-2" tabindex="-1"></a><sp