class="anchor" aria-label="anchor" href="#arg-always-merge-sbs"></a></dt>
<dd><p>If <code>TRUE</code> merge adjacent SBSs as DBSs
regardless of VAFs and regardless of the value of <code>max.vaf.diff</code>.</p></dd>


<dt id="arg-chr-names-to-process">chr.names.to.process<a class="anchor" aria-label="anchor" href="#arg-chr-names-to-process"></a></dt>
<dd><p>A character vector specifying the chromosome
names in VCF whose variants will be kept and processed, other chromosome
variants will be discarded. If <co