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

Will McLaren wm2 at ebi.ac.uk
Wed Oct 9 11:58:27 BST 2013


Thanks, I'll get the link updated.

Will


On 9 October 2013 11:52, Tjaart de Beer <tjaart at ebi.ac.uk> wrote:

> Hi Will,
>
> Thanks for the answers. I'll look at the two options and see which one
> suits me best for now. By the way the link for installing a local mirror
> from this page
>
> http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#local
>
> "...installing a local mirror, see HERE."
>
> which points to
>
> http://www.ensembl.org/info/docs/webcode/install/ensembl-data.html
>
> results in an error.
>
> Thanks again,
>
> Tjaart
>
> > Hi Tjaart,
> >
> > Firstly, thanks for finding this, there was an odd bug with patched
> > chromosome regions that was causing this error. I've fixed it on the CVS
> > branch for 73 - if you update your ensembl-variation checkout, or rerun
> > the
> > installer if you used that, you should pick up the fixed code.
> >
> > Secondly, while it is possible to use rsIDs as input, I wouldn't
> recommend
> > doing this on such a large scale. Each rsID has to be looked up in the
> > database to find its genomic location and alleles. So even though you are
> > using the cache, the VEP will be querying the public Ensembl database for
> > each rsID, and then using the cache for it's consequence predictions.
> >
> > If you do need to query in this way, I'd suggest setting up a local
> mirror
> > of the Ensembl variation database, see
> > http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#local
> >
> > Another alternative would be to extract the corresponding VCF entries for
> > your rsIDs from our VCF dumps (
> > ftp://ftp.ensembl.org/pub/release-73/variation/vcf/homo_sapiens/), using
> > something like vcftools (and the --snps flag). You can either get the
> > version of the VCF with consequences, which may save you running the VEP
> > at
> > all, or get the version without consequences and run this through the VEP
> > if you need more than the basic consequence information.
> >
> > Hope that helps
> >
> > Will McLaren
> > Ensembl Variation
> >
> >
> > On 8 October 2013 16:55, Tjaart de Beer <tjaart at ebi.ac.uk> wrote:
> >
> >> 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
> >>
> >>
> >>
> >> _______________________________________________
> >> Dev mailing list    Dev at ensembl.org
> >> Posting guidelines and subscribe/unsubscribe info:
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> >> Ensembl Blog: http://www.ensembl.info/
> >>
> >
>
>
> --
> 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
>
>
>
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