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

[DUTTA Prasun]

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<tel:%2B447438743406>
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