<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi all<div class=""><br class=""></div><div class="">Just come across a strange issue with VEP. We’re re-annotating a whole bunch of files with a reference genome that contains some of the lowercase masked regions, and we’re getting them filtered out by VEP when using the —check-ref warning. This was a surprise as the variant callers were using the exact same reference genome but referencing them as uppercase. </div><div class=""><br class=""></div><div class="">Would it be possible to have a kind of non-strict —checkref that is OK with lowercase base letters in the reference, so long as it’s the same base letter? Or am I doing this totally wrong?</div><div class=""><br class=""></div><div class="">All the best</div><div class="">Stuart<br class=""><div class="">
<div class=""><div class="">—</div><div class=""><font color="#4f0500" class=""><b class="">Stuart Watt, PhD</b></font></div><div class=""><font color="#4f0500" class="">Scientific Research Associate, Princess Margaret Cancer Centre</font></div><div class=""><font color="#4f0500" class="">MaRS Centre, 101 College Street<br class="">Toronto Medical Discovery Tower, Room 9-302<br class="">Toronto, Ontario, Canada M5G 1L7</font></div><div class=""><font color="#4f0500" class=""><a href="mailto:stuart.watt@uhnresearch.ca" class="">stuart.watt@uhnresearch.ca</a><br class="">416-634-8816</font></div></div>
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