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<div class="moz-cite-prefix">Hello Will,<br>
<br>
thanks for your quick response. <br>
<br>
I would want to stay on version 66, because our NGS pipeline is
built around this release and I would like to keep all our results
as consistent as possible.<br>
<br>
But now back to my problem: I tried what you said and set up two
installations for VEP with ensembl 66 and for ensembl 69
(according to the link you provided), both times using the install
script to also setup the corresponding API and cache version.
First of all I thought I dowloaded VEP version 2.4 as stated by
the link description on the website and the README file inside the
tar.gz. But I looked into the source code and help screen and the
VEP script is actually version 2.6. This is kind of confusing,
because if I understood you correctly each VEP version should best
be used with a certain API version. <br>
<br>
I only saw ensembl gene IDs when I used Ensembl version 69 API,
but never with Ensembl API version 66. The VEP version did not
matter and the --gene option wasn't available in any of the two
VEP versions. <br>
<br>
I also noticed that, when using version 66 (with VEP 2.7 and
VEP2.6) I get an error message that says<br>
Can't use string ("21 26960070 rs116645811 G A
. . "...) as a SCALAR ref while "strict refs" in use at
variant_effect_predictor.pl line 1550<br>
<br>
When I change this line in the source from <br>
$output = $$line;<br>
to<br>
$output = $line;<br>
it works, but then it doesn't work for API version 69 anymore.
Maybe this is a bit off topic though. <br>
<br>
So I think now I have two questions regarding the Gene Ids: <br>
<br>
1) How can I download the actual VEP 2.4 script to try out what
you suggested? The link on the official website only lets me
download VEP2.6.<br>
2) To me it seems that the API version is the cause for my
problem, because I get Gene IDs when I use ensembl 69 with any of
the two VEP versions. Is there any explaination for this? <br>
<br>
And a third question about the cache: What is included in the
cache and where can I find information on how to use the local
database to add custom annotations? I would really like to use the
local cache only, but I always used our local database because I
figured that you couldn't have possibly stored all information for
all possible variants in a single 2GB cache file, or could you? <br>
<br>
<br>
Best wishes & sorry for all the text and all the questions :)<br>
Sebastian<br>
<br>
On 08.01.2013 14:17, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX10WjGoYckkHRwQ_3vjx2HmbJHyQMMUDt4ivjyA+OV5Wg@mail.gmail.com"
type="cite">
<div dir="ltr">Hello Sebastien,
<div><br>
</div>
<div>Thanks for the detailed report.</div>
<div><br>
</div>
<div style="">I think the problem may be caused by using an
older version of the API. The latest version of the script
(2.7) should be used with version 69 of the Ensembl API.</div>
<div style=""><br>
</div>
<div style="">If you need to use version 66 of the API (for
example if you are unable to upgrade the database you are
using), you should use the appropriate script version with
this. You can see which versions go together here:</div>
<div style=""><br>
</div>
<div style=""><a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download">http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download</a><br>
</div>
<div style=""><br>
</div>
<div style="">
As an aside, you may find that the latest version of the VEP
gives you everything you need in the cache files available
from us without having to use a local database. However, of
course if you are using a local database for custom
annotations, you should continue to do so.</div>
<div style=""><br>
</div>
<div style="">Regards</div>
<div style=""><br>
</div>
<div style="">Will McLaren</div>
<div style="">Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 8 January 2013 11:59, Sebastian
Ginzel <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:sginze2s@inf.h-brs.de" target="_blank">sginze2s@inf.h-brs.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Dear
Ensembl-Developer Team,<br>
<br>
I want to use the Variant Effect Predictor standalone script
to annotate my VCF file for further processing and I need
the variants to have Ensembl Gene IDs.<br>
<br>
Unfortunatly the --gene option is not working and results in
this error message:<br>
<br>
Unknown option: gene<br>
ERROR: Failed to parse command-line flags<br>
<br>
Without the --gene option everything runs through perfectly,
but no Ensembl Gene IDs show up in the output although the
documentation avaiable at <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/variation/vep/vep_script.html#output"
target="_blank">http://www.ensembl.org/info/docs/variation/vep/vep_script.html#output</a>
suggests that the output of ENSG IDs is forced when using
the --cache option (which I also use). A quick check of the
source code of the <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>
script showed me, that the --gene option seems not to be
implemented anymore.<br>
<br>
I saw that there was somebody mentioning the removal of the
--gene option in the mailing list archives following a
thread that started on 5th December 2012 09:12:48. But it
doesn't mention anything like my problem.<br>
<br>
That leaves me with two questions:<br>
<br>
1) What happend to the --gene option and can anyone
reproduce this?<br>
2) How can I force the population of the Ensembl Gene ID
column when --cache is also not working?<br>
<br>
<br>
Best wishes,<br>
Sebastian Ginzel<br>
<br>
PS: Here is what I did to setup VEP on my Ubuntu 12.04
system with perl v5.14.2.<br>
<br>
I downloaded and setup the latest VEP version 2.7 (<a
moz-do-not-send="true"
href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/variant_effect_predictor.tar.gz?view=tar&root=ensembl&pathrev=branch-ensembl-69"
target="_blank">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-tools/scripts/variant_effect_predictor.tar.gz?view=tar&root=ensembl&pathrev=branch-ensembl-69</a>
- MD5Sum ab780dcb0267e5872f85ebe2ff4837f5)<br>
<br>
"perl variant_effect_predictor.pls --help" shows me that I
actually use the 2.7 version.<br>
<br>
I also downloaded some plugins through GIT using:<br>
git clone "<a moz-do-not-send="true"
href="https://github.com/ensembl-variation/VEP_plugins"
target="_blank">https://github.com/ensembl-variation/VEP_plugins</a>"<br>
<br>
I used this command line to call the script:<br>
<br>
perl /home/sginze2s/vep/lib/vep/bin/variant_effect_predictor/<a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>
-i /home/sginze2s/vep/lib/vep/sample1.vcf -o /tmp/bla.vcf
--cache --dir /home/sginze2s/vep/lib/vep/bin/cache
--prefetch --no_adaptor_cache --write_cache --strip
--everything --gmaf --xref_refseq --failed 1 --fork 4
--vcf --format vcf --no_progress --check_existing
--check_svs --plugin Condel,/home/sginze2s/vep/lib/vep/bin/cache/Plugins/config/Condel/config
--plugin Blosum62 --plugin Downstream --species homo_sapiens
--db_version=66 --host <a moz-do-not-send="true"
href="http://bio.inf.h-brs.de" target="_blank">bio.inf.h-brs.de</a>
--user ensembl --password ******* --port 13306
--force_overwrite --quiet --gene<br>
<br>
I use Ensembl API version 66 and use the PERL5LIB variable
to link to it.<br>
PERL5LIB=/lib/ensembl_66/ensembl-functgenomics/modules:/lib/ensembl_66/ensembl-variation/modules:/lib/ensembl_66/ensembl-compara/modules:/lib/ensembl_66/ensembl/modules:/lib/bioperl-1.2.3:/lib/bioperl-1.5.2_102_Matrix<br>
<br>
<br>
<br>
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</blockquote>
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