 class="op">)</span> 10 -f gtseq15_loci.fasta -L bamlist.txt --haplotype-length 0 -kwVa --no-mnps --no-complex <span class="op">&gt;</span> satro384_noMNP_noComplex_noPriors.vcf</span></code></pre></div>
</div>
<div id="runhaplot" class="section level3">
<h3 class="hasAnchor">
<a href="#runhaplot" class="anchor"></a>runHaplot</h3>
<p>After the above is done, the file <code>satro384_noMNP_noComplex_noPriors.vcf</code> can be filtered, if desired, to make sure that everything in it has a solid SNP. Then that 