<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 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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