[ensembl-dev] Variant Effect Predictor --gene option not working

[Will McLaren]

Hello Sebastien,

Thanks for the detailed report.

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.

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:

http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download

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.

Regards

Will McLaren
Ensembl Variation


On 8 January 2013 11:59, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:

> Dear Ensembl-Developer Team,
>
> 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.
>
> Unfortunatly the --gene option is not working and results in this error
> message:
>
> Unknown option: gene
> ERROR: Failed to parse command-line flags
>
> Without the --gene option everything runs through perfectly, but no
> Ensembl Gene IDs show up in the output although the documentation avaiable
> at http://www.ensembl.org/info/**docs/variation/vep/vep_script.**
> html#output<http://www.ensembl.org/info/docs/variation/vep/vep_script.html#output>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
> variant_effect_predictor.pl script showed me, that the --gene option
> seems not to be implemented anymore.
>
> 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.
>
> That leaves me with two questions:
>
> 1) What happend to the --gene option and can anyone reproduce this?
> 2) How can I force the population of the Ensembl Gene ID column when
> --cache is also not working?
>
>
> Best wishes,
> Sebastian Ginzel
>
> PS: Here is what I did to setup VEP on my Ubuntu 12.04 system with perl
> v5.14.2.
>
> I downloaded and setup the latest VEP version 2.7 (
> 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<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>- MD5Sum ab780dcb0267e5872f85ebe2ff4837
> **f5)
>
> "perl variant_effect_predictor.pls --help" shows me that I actually use
> the 2.7 version.
>
> I also downloaded some plugins through GIT using:
> git clone "https://github.com/ensembl-**variation/VEP_plugins<https://github.com/ensembl-variation/VEP_plugins>
> "
>
> I used this command line to call the script:
>
> perl /home/sginze2s/vep/lib/vep/**bin/variant_effect_predictor/v**
> ariant_effect_predictor.pl <http://variant_effect_predictor.pl> -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 bio.inf.h-brs.de --user ensembl --password *******
> --port 13306 --force_overwrite --quiet --gene
>
> I use Ensembl API version 66 and use the PERL5LIB variable to link to it.
> 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
>
>
>
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