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

[Sebastian Ginzel]

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 
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 
- MD5Sum ab780dcb0267e5872f85ebe2ff4837f5)

"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"

I used this command line to call the script:

perl 
/home/sginze2s/vep/lib/vep/bin/variant_effect_predictor/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