<span id="mailbox-conversation"><div>Hi all,</div>
<div><br></div>
<div>I just figured it out - I was using a RankFilter. Strangely, I'd been using the same one in v77 and it wasn't removing them - perhaps the severity ordering changed/wasn't working before? Anyway, makes sense, thanks!</div></span><div class="mailbox_signature"><br></div>
<br><br><div class="gmail_quote"><p>On Fri, May 22, 2015 at 8:06 AM, Anja Thormann <span dir="ltr"><<a href="mailto:anja@ebi.ac.uk" target="_blank">anja@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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Konrad,<div><br></div>
<div>I ran the following command using ensembl-tools (release/79) and human cache files homo_sapiens_vep_79_GRCh37.tar.gz.</div>
<div><br></div>
<div>perl variant_effect_predictor.pl --cache --offline -i test_vep_input.txt -o test_vep_output.txt -force_overwrite --no_stats --assembly GRCh37 --regulatory</div>
<div><br></div>
<div>where input:</div>
<div>1 13372 13372 G/C + testvariant</div>
<div><br></div>
<div>and output:</div>
<div>testvariant 1:13372 C - ENSR00001576075 RegulatoryFeature regulatory_region_variant - - - - - - IMPACT=MODIFIER;BIOTYPE=CTCF_binding_site</div>
<div><br></div>
<div>----------------</div>
<div>Running not offline and using --everything also returns overlap with a regulatory feature:</div>
<div><div>testvariant 1:13372 C - ENSR00001576075 RegulatoryFeature regulatory_region_variant - - - - - - IMPACT=MODIFIER;BIOTYPE=CTCF_binding_site</div></div>
<div><br></div>
<div><br></div>
<div>Could you please try and refresh all your ensembl APIs and try running the analysis again? At the moment I cannot reproduce the problem.</div>
<div><br></div>
<div>Thank you,</div>
<div>Anja</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div>
<br><div>
<div>On 21 May 2015, at 15:17, Konrad Karczewski wrote:</div>
<br class="Apple-interchange-newline"><blockquote type="cite">
<span id="mailbox-conversation">Yeah, I was surprised as well. Removing the histones makes sense: could account for most of the difference, but it went from 1916763 to 0(!). Even in a biased set, would have expected a few by chance.<div><br></div>
<div>If you'd like more examples, it's the ExAC dataset (<a href="ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz">ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz</a>) - this one was annotated with v77 so the ones with RegulatoryFeatures (albeit 2M of them) may give you a starting point.</div>
<div><br></div>
<div>Thanks for looking into it!</div></span><div class="mailbox_signature"><br></div>
<br><br><div class="gmail_quote">
<p>On Thu, May 21, 2015 at 10:02 AM, Daniel Zerbino <span dir="ltr"><<a href="mailto:zerbino@ebi.ac.uk">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">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 href="mailto:zerbino@ebi.ac.uk">zerbino@ebi.ac.uk</a>></span>
wrote:<br></p>
<blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; position: static; z-index: auto; ">
<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 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=""></div>
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