[ensembl-dev] ensembl genomes VEP

[Will McLaren]

Hi Seth,

A couple of possible pitfalls here. Firstly, e!Genomes release numbers are
different to Ensembl version numbers, so you need to specify the correct
--cache_version number. Secondly, the default database connection options
connect you to ensembldb.ensembl.org, which hosts our vertebrate genomes;
you can switch to using the e!Genomes server with --genomes or use
--offline to avoid the DB connection entirely.

Here's what I did to check it works:

> curl
ftp://ftp.ensemblgenomes.org/pub/protists/current/vep/plasmodium_berghei_vep_25_May_2010.tar.gz
> ~/.vep/pb.tgz
> tar -C ~/.vep/ -xzf ~/.vep/pb.tgz
> echo "1 358941 358941 C/T 1" | perl variant_effect_predictor.pl -force
-offline -species plasmodium_berghei -cache_version 25 -o STDOUT | grep -v #
1_358941_C/T    1:358941        T       PBANKA_010970   PBANKA_010970:mRNA
     Transcript      downstream_gene_variant -       -       -       -
  -
        -       IMPACT=MODIFIER;DISTANCE=3801;STRAND=-1
1_358941_C/T    1:358941        T       PBANKA_010960   PBANKA_010960:mRNA
     Transcript      upstream_gene_variant   -       -       -       -
  -
        -       IMPACT=MODIFIER;DISTANCE=2312;STRAND=1
1_358941_C/T    1:358941        T       PBANKA_010930   PBANKA_010930:mRNA
     Transcript      upstream_gene_variant   -       -       -       -
  -
        -       IMPACT=MODIFIER;DISTANCE=2782;STRAND=-1
1_358941_C/T    1:358941        T       PBANKA_010940   PBANKA_010940:mRNA
     Transcript      upstream_gene_variant   -       -       -       -
  -
        -       IMPACT=MODIFIER;DISTANCE=1008;STRAND=-1
1_358941_C/T    1:358941        T       PBANKA_010950   PBANKA_010950:mRNA
     Transcript      missense_variant        4       4       2       L/F
  Ctt/Ttt  -       IMPACT=MODERATE;STRAND=1

HTH

Will McLaren
Ensembl Variation

On 20 March 2015 at 15:23, Seth Redmond <snr at sanger.ac.uk> wrote:

>   I’m having some trouble getting the VEP to work on a P.berghei cache
> downloaded from ensemblgenomes (
> ftp://ftp.ensemblgenomes.org/pub/protists/current/vep/). Though it
> doesn’t seem to be throwing any errors and is apparently reading in the
> correct files for each chromosome, I’m still not getting any transcripts
> found for any loci.
>
>  Could be a version issue, but is there any way to be sure of the ensembl
> version from the cache itself? or is there somewhere else I should be
> looking?
>
>  thanks
>
>  -s
>
>
>  --
>  Seth Redmond
> Senior Bioinformatician
> Parasite Genomics
>   Wellcome Trust Sanger Institute
>   Genome Campus
>   Hinxton CB10 1SA
> snr at sanger.ac.uk
>
>
>
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