alue</h2>


<p>A <strong>list</strong> of elements:</p><ul><li><p><code>catalog</code>: The ID (small insertions and deletions) catalog with
attributes added. See <code><a href="as.catalog.html">as.catalog</a></code> for details.</p></li>
<li><p><code>discarded.variants</code>: <strong>Non-NULL only if</strong> there are variants
that were excluded from the analysis. See the added extra column
<code>discarded.reason</code> for more details.</p></li>
<li><p><code>annotated.vcfs</code>:
<strong>Non-NULL only 