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<div class="moz-cite-prefix">Wait a minute, *none* of them do?
That's something else entirely...<br>
<br>
Now, ExAC is a somewhat biased set in that it is pulled down from
exon sequencing, and a difference between the old and the new
build is that regions with the histone marks associated to
transcription are no longer annotated as "regulatory". This is
what you see at your locus 1:13372, on e75, where there used to be
mostly "gene associated" annotations across cell types. <br>
<br>
However, 0 hits across 10M sounds very suspicious. For example,
the locus you describe happens to be on the edge of a CTCF feature
(the actual binding site is a bit farther on the 5'), so it should
technically have been reported. <br>
<br>
We'll investigate...<br>
<br>
On 5/21/15 1:56 PM, Konrad Karczewski wrote:<br>
</div>
<blockquote cite="mid:1432213000301.ead5fc46@Nodemailer" type="cite">
<div>Hi Daniel,</div>
<div><br>
</div>
<div>Ah ok great thanks! Thing is though: now none of the 10M
variants in ExAC overlap RegulatoryFeatures. Is that expected? I
would have expected at least a few...</div>
<div class="mailbox_signature">
<br>
-Konrad</div>
<br>
<br>
<div class="gmail_quote">
<p>On Thu, May 21, 2015 at 2:17 AM, Daniel Zerbino <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:zerbino@ebi.ac.uk" target="_blank">zerbino@ebi.ac.uk</a>></span>
wrote:<br>
</p>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
<div class="moz-cite-prefix">Hello Konrad,<br>
<br>
this is because on release 79 we replaced the old
regulatory build with the newer version (which we had
released for GRCh38 in v76).<br>
<br>
There would definitely be some moving around of features
as both builds are very different in the way they are
computed.<br>
<br>
Regards,<br>
<br>
Daniel<br>
<br>
On 5/21/15 5:28 AM, Konrad Karczewski wrote:<br>
</div>
<blockquote
cite="mid:20150521042917.1CEAB132A40_55D5F1DB@hx-mx2.ebi.ac.uk"
type="cite"> Hi Will, everyone,
<div class=""><br class="">
</div>
<div class="">Are RegulatoryFeature annotations expected
to have the same results in VEP v79 (GRCh37) as previous
versions (e.g. v77)? When annotating the ExAC VCF, the
older versions included many ENSR* annotations, but
v79's do not (same command including --everything both
times). For instance, the following variant used to
overlap ENSR00000528767 but does not seem to in my most
recent version:</div>
<div class=""><br class="">
</div>
<div class="">1 13372 . G C</div>
<div class=""><br class="">
</div>
<div class="">Any idea why this might be happening? All
other annotations seem fine.<br class="">
<div class=""><br class="webkit-block-placeholder">
</div>
<div class="">
<div style="color: rgb(0, 0, 0); letter-spacing:
normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal;
orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px;" class="">Thanks!<br
class="Apple-interchange-newline">
-Konrad</div>
</div>
</div>
<br class="">
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