<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<br>
Hi Dani,<br>
<br>
I'm sorry to hear you are having this problem, but we are unable to
replicate it. <br>
<br>
We have observed problems with FASTA index corruption which would
cause this issue - try deleting
$HOME/.vep/[species]/[assembly]/[fastafile].index (or .fai) and
re-running VEP to regenerate it. <br>
<br>
Make sure you are using a >=1.6 version of BioPerl - older
versions can have this problem with large files. The VEP installer
installs 1.6.1 for you.
<div style="font-size:12.8000001907349px"><br>
</div>
Also, try re-installing the API to ensure you are using the precise
version we tested.<br>
<br>
I hope this helps,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 08/01/2016 12:54, Daniel Borras
wrote:<br>
</div>
<blockquote
cite="mid:560912324.989586.1452257664129.JavaMail.zimbra@genomescan.nl"
type="cite">
<div style="font-family: tahoma,new york,times,serif; font-size:
12pt; color: #000000">
<div data-marker="__QUOTED_TEXT__">
<div style="font-family: tahoma,new york,times,serif;
font-size: 12pt; color: #000000">
<div>Dear Sir, Madame,<br>
</div>
<br>
<div>My name is Daniel Borras and I am currently working
with your tool Variant Effect Predictor. I usually input
HGVS variants obtained from other sources to annotate
their effect. However I noticed an unexpected behaviour
when it comes to duplications. When feeding VEP with an
HGVS duplication this is transformed to an insertion,
please the real output below. According to HGVS
recommendations, duplications are reported differently
than insertions, let me quote HGVS recommendations:
g.5dupT (or g.5dup, <strong><em>not g.5_6insT</em></strong>)
. This wouldn't be a big issue if it wasn't because for
downstream analysis the annotation of the variant changes
making previous comparisons and checks to fail since the
variant description is different. I believe that this
behaviour should be patched, probably is not too
complicated to fix, and will make VEP to report correct
duplications in HGVS notation.<br>
</div>
<br>
<div>The results are I obtained are:<br>
</div>
<div>Input: <strong>NM_001009944.2:c.4248dup</strong><br>
</div>
<div>Output:<strong>NM_001009944.2:c.4248_4249insT</strong><br>
</div>
<div>Row: chr16 2160919 <strong>NM_001009944.2:c.4248dup</strong>
C CA . .
A|frameshift_variant|HIGH|PKD1|5310|Transcript|NM_001009944.2|protein_coding|15/46||<strong>NM_001009944.2:c.4248_4249insT</strong>|NP_001009944.2:p.Gly1417TrpfsTer14|4457-4458|4248-4249|1416-1417|-/X|-/T|||-1|insertion|||YES|||NP_001009944.2||||rseq_mrna_nonmatch&rseq_cds_mismatch&rseq_ens_match_wt|||||||||||||||||||||</div>
<br>
<div>The results were obtained by using:<br>
</div>
<div>VEP version: ensembl-tools-release-80</div>
<div>Assembly: GRCh37</div>
<div>Cache_version: 80</div>
<div>Port: 3337</div>
<br>
<br>
<div>Best,<br>
</div>
<div>Dani<br>
</div>
<br>
</div>
<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>