nes whose reads appear in the assemblies. The VCF is merely used as a way of defining positions to extract. Still, since the content of microhaplotype is based on the variant positions listed in the VCF file, it is crucial for the VCF file to only contain highly reliable variant sites.</li>
</ol>
<p>We describe here the workflow that we use to get these two necessary files from the short-read amplicon sequencing data that come off our Illumina Mi-seq. This workflow can be tweaked and tailored for your own d