-mismatches"></a></dt>
<dd><p>Deprecated. If there are ID variants whose <code>REF</code>
do not match the extracted sequence from <code>ref.genome</code>, the function
will automatically discard these variants and an element
<code>discarded.variants</code> will appear in the return value. See
<code><a href="AnnotateIDVCF.html">AnnotateIDVCF</a></code> for more details.</p></dd>


<dt id="arg-return-annotated-vcfs">return.annotated.vcfs<a class="anchor" aria-label="anchor" href="#arg-return-annotated-vcfs">