[ensembl-dev] build a cache from a GTF file query

[Will McLaren]

Hello,

It might be that the GTF file you have supplied is not being parsed
correctly by gtf2vep.pl. If you add --verbose to your gtf2vep.pl command
you should hopefully see some warnings that might give you a clue what is
lacking in your file.

Our new beta release of VEP, ensembl-vep, includes much improved
functionality for using annotations in GFF/GTF, see
https://github.com/Ensembl/ensembl-vep for details. This beta will become
the official release of VEP in the coming weeks.

Regards

Will McLaren
Ensembl Variation

On 6 March 2017 at 14:57, DUTTA Prasun <s0928794 at sms.ed.ac.uk> wrote:

>
> Hi,
>
>
> I was trying to build a cache from a GTF file that corresponds to a water
> buffalo (no ensemble database/annotation available, only available in NCBI
> Genome database) and was following the underwritten commands according to
> your website (http://www.ensembl.org/info/docs/tools/vep/script/vep_
> cache.html):
>
>
> perl gtf2vep.pl -i GCF_000471725.1_UMD_CASPUR_WB_2.0_genomic.revised.gtf
> -f GCF_000471725.1_UMD_CASPUR_WB_2.0_genomic.fa -d 87-s buffalo
>
>
>
> perl variant_effect_predictor.pl -offline -i varfiltered_F3_M3_merged_0h_
> 7h_sorted_samtools_with_variant_type_without_INDEL_bcftools_snpSift.vcf
> --species buffalo -o varfiltered_F3_M3_merged_0h_7h_sorted_samtools_with_
> variant_type_without_INDEL_bcftools_snpSift_VEP.vcf
>
>
> But, I am getting a following error:
>
>
> ERROR: Cache directory /nfs_netapp/s0928794/.vep/buffalo not found
>
> I checked '/nfs_netapp/s0928794/.vep/' and indeed there was no buffalo
> folder there. Kindly let me know what am I missing and what should I do so
> that I can successfully use VEP to annotate my variants that I have for
> water buffalo.
>
>
>
> Regards,
> Prasun Dutta, M.Sc. (Bioinformatics)
> PhD Student, Developmental Biology Division (Hume Group)
> The Roslin Institute, The University of Edinburgh, Scotland, UK
> M: +447438743406 <+44%207438%20743406> <%2B447438743406>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
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