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Hi Cyriac,<br>
<br>
The --shift_hgvs option is available in v79, so do try it and let us
know if the results are not what you expect.<br>
<br>
All the best,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 22/05/2015 16:46, Cyriac Kandoth
wrote:<br>
</div>
<blockquote
cite="mid:20150522154723.6D16C22F577_55F4F8BB@hx-mx1.ebi.ac.uk"
type="cite">
<div dir="ltr">Thanks very much Sarah. This is good to know. We're
using VEP v79 in offline more, on command line, on GRCh37 loci.
Do we need to update to v80, to be able to use the --shift-hgvs
option?
<div><br>
</div>
<div>Cheers!</div>
<div><br>
</div>
<div>~Cyriac</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, May 22, 2015 at 4:39 AM, Sarah
Hunt <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:seh@ebi.ac.uk" target="_blank">seh@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> <br>
Hi Cyriac,<br>
<br>
Thanks for the query - could you supply a bit more
information?. Are you using VEP through the web site, REST
or by command line? Is your data on GRCh37 or GRCh38? <br>
<br>
Prior to e!80, non-shifted desriptions were our default
and the --shift_hgvs option had to be selected when using
the command line script to produce 3' shifted HGVS
annotation. As of e!80, shifted descriptions will be the
default and there will be a command line option to turn
them off. <br>
<br>
The GRCh38 website was updated to e!80 yesterday and the
GRCh37 site will be updated shortly.<br>
<br>
Best wishes,<br>
<br>
Sarah
<div>
<div class="h5"><br>
<br>
<div>On 21/05/2015 20:29, Cyriac Kandoth wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">
<div>Here is a VCF-format example of an insertion
within a tandem repeat region, that reports
HGVSp = p.Ala771_Tyr772ins.</div>
<div>17 37880984 . A ATACGTGATGGCT . . .</div>
<div><br>
</div>
<div>HGVS, at least for deletions, states "the
most 3' position possible is arbitrarily
assigned to have been changed". This is
different from the oft-used convention of
"left-shifting" indels. So what's the correct
solution here?</div>
<div><br>
</div>
<div>This one's pretty complicated and I'm still
trying to get my head around it. But I would
love to hear from someone who worked on
implementing HGVS notations into VEP.<br>
</div>
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>~Cyriac</div>
</div>
<br>
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