[ensembl-dev] VEP exception when using a specific rsid

[Tjaart de Beer]

Hi all,

I just installed VEP to have a look at some human variant data. I have
about 550,000 rsids. As far as I understand from the documentation an rsid
on its own should be enough. When I run my rsids I get the following
error:

-------------------- EXCEPTION --------------------
MSG: SEQ_REGION_NAME argument is required
STACK Bio::EnsEMBL::Slice::new
/home/tjaart/my_genes/variant_effect_predictor/Bio/EnsEMBL/Slice.pm:149
STACK Bio::EnsEMBL::Variation::Utils::VEP::get_slice
/home/tjaart/my_genes/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:3306
STACK Bio::EnsEMBL::Variation::Utils::VEP::cache_transcripts
/home/tjaart/my_genes/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:3596
STACK Bio::EnsEMBL::Variation::Utils::VEP::fetch_transcripts
/home/tjaart/my_genes/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2837
STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons
/home/tjaart/my_genes/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1180
STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences
/home/tjaart/my_genes/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1125
STACK main::main variant_effect_predictor.pl:360
STACK toplevel variant_effect_predictor.pl:198
Date (localtime)    = Tue Oct  8 16:43:28 2013
Ensembl API version = 73

As far as I could make out this means that the variant is not in Ensembl.
In my test set I have traced it to rs7289804 which does not occur in
Ensembl (doing a web search).

I was wondering if there is a way around this with some kind of flag to
ignore rsids for which there is not enough data or it not being present? I
couldn't find such a flag in the documentation.

My command is:

perl variant_effect_predictor.pl -i ../test.dat --cache --coding_only
--filter coding_change --force_overwrite

My input file contains no extra line breaks or any strange characters.

Any help would be appreciated. Thanks!


--
Dr. Tjaart de Beer
Thornton group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom