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<p>It&#x27;s recommended to have at least 10X-12X depth to get decent structural variant calls
(definitely read that in a paper that I would like to link here, but I can&#x27;t seem to find
it). If your data already has a minimum of 10X for each individual, great! Feel free to use
variant callers like <code v-pre>naibr</code> and <code v-pre>leviathan</code> to identify structural variants. Hwoever, if
variant callers like <code v-pre>naibr</code> and <code v-pre>leviathan</code> to identify structural variants. However, if
you opted to sequence more individuals at lower coverage (lcWGS is often between 0.5-5X),
then calling structural variants in individuals may be a challenge.</p>
<doc-anchor-target id="the-solution">
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<figcaption class="caption">PCA of Alosa sapidissima (SNPs from low-coverage haplotag dataset)</figcaption>
</figure>
</p>
<p>Given these results, a sensible pooling strategy would be:</p>
<p>Given these results, a sensible pooling strategy may be:</p>
<ul>
<li><strong>Pool 1</strong>: Miramichi samples</li>
<li><strong>Pool 2</strong>: Annapolis samples</li>
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