n probability and the negative strand base modification probability must be above the pass threshold.</li>
</ol>
<p>See <a href="./advanced_usage.html">Advanced Usage</a> for details on all the options.</p>
<h2 id="description-of-hemi-methylation-patterns"><a class="header" href="#description-of-hemi-methylation-patterns">Description of hemi-methylation patterns</a></h2>
<p>The <code>modkit pileup-hemi</code> command aggregates a pair of base modification calls at each reference motif position
for each doub