<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">ok, thanks<div><br></div><div>yuan<br><div style=""><div>On 22 May 2014, at 09:12, Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">Hi Yuan,<div><br></div><div>--most_severe doesn't consider regulatory variants, though it probably should. However, this uses a method in the API that is also used in places by the webcode, so I am wary of changing it.</div>
<div><br></div><div>I'd definitely recommend using --pick if you must have one consequence per variant.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 22 May 2014 05:44, Yuan Chen <span dir="ltr"><<a href="mailto:yuan@sanger.ac.uk" target="_blank">yuan@sanger.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Will,<br>
<br>
For this variant : 2 11600 . A T<br>
<br>
if I use pick with regulatory, I got :<br>
2 11600 . A T 128 PASS CSQ=T||MA0139.1|MotifFeature|TF_binding_site_variant|||||||Jaspar_Matrix_CTCF:MA0139.1|18|N|-0.015||-1<br>
<br>
if I use most_severe with regulatory, I got :<br>
2 11600 . A T 128 PASS CSQ=||||intergenic_variant||||||||||||<br>
<br>
Do most_severe flag considering regulatory variant ?<br>
<br>
Thanks for your help !<br>
<span class="HOEnZb"><font color="#888888"><br>
yuan</font></span><br>_______________________________________________<br>
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<br></blockquote></div><br></div>
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