/li>
<li>We thought that <code>GATK's Unified Haplotype Caller</code> might deliver us from the bioinformatic hell we were experiencing, but alas, with the super-high read depths at some of the fragments in our amplicon sequencing data, GATK was brought to its knees and didn’t offer a viable solution. It appears that the HaplotypeCaller is trying to solve a much harder problem than just extracting short-read haplotypes.</li>
</ul>
<p>After a few months of this, we realized that there is no software tailor