<p>Dear everyone,</p>

<p>I have been asked to comment on an experiment design that involves WES or WGS of cancer cell lines which lack matched normal.</p>

<p>I know that this design is far from ideal, but I was wondering if there are people who have already stream-lined it (to the extent possible of course). I can think of a couple of common variation filters to keep out the germline variants, but I am not sure how to go beyond.</p>

<p>I am sorry if this is a duplicate question; I couldn&#39;t find a related hit.</p>

<p>Thank you,</p>

<p>Noushin</p>

<p>The bottom line is that without a matched normal, you&#39;re just not going to be able to call the somatic status for the vast majority of sites. That said, you can winnow down a list to those you *suspect* are somatic. Some ideas:</p>

<ul>
	<li>Weed out sites with high frequency in the population</li>
	<li>If your tumor is very impure, you can take advantage of the fact that the frequencies of somatic variants will be shifted away from 50%/100%</li>
</ul>
