[ensembl-dev] ./vep offline problem

[Sabrina Legoueix-Rodriguez]

Dear all,

I have installed on my machine your recent vep API locally to use a home 
made genome in order to get SNPs annotations.

I used the instructions on these pages:
http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#offline
http://www.ensembl.org/info/docs/tools/vep/script/index.html

My inputs are:
-> a home made reference genome in fasta file
-> a .VCF file with SNPs list on that genome
-> a .GTF file with genome annotations

My goal is to use vep to generate a .vep file with functionnal 
annotations of my SNPs.

For instance:

my gtf is:
tig00000004_pilon_pilon    Pacbio    gene    231183    234374 .    +    
.    gene_id "A";
tig00000004_pilon_pilon    Pacbio    transcript    231183 234374    .    
+    .    gene_id "A";transcript_id "A";
tig00000004_pilon_pilon    Pacbio    CDS    231183    234374    . +    
.    gene_id "A";transcript_id "A";
tig00000004_pilon_pilon    Pacbio    exon    231183    234374 .    +    
.    gene_id "A";transcript_id "A";

( I also tried with a .gff)

my vcf is:
##...
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO FORMAT  
A_ATTACTCG
tig00000004_pilon_pilon 232205  .       G       A       9881.15 . 
AC=8;AF=0.800;AN=10;DP=245;FS=0.000;MLEAC=8;MLEAF=0.800;MQ=60.05;QD=25.82;SOR=0.983 
GT:AD:DP:GQ:PL  0:9,0:9:99:0,247

=> this snp should be found in the gene "A"

To prepare the gtf (or also .gff), I used:
grep -v "^#" test.gtf  | sort -k1,1 -k4,4n -k5,5n | bgzip -c > test.gtf.gz
tabix -p gtf test.gtf.gz

my command line is:
./vep -i test.vcf -gtf test.gtf.gz -fasta ref.fasta --force_overwrite
or
./vep -i test.vcf -gff test.gff.gz -fasta ref.fasta --force_overwrite

The result file is:
#Uploaded_variation     Location        Allele  Gene    Feature 
Feature_type    Consequence     cDNA_position   CDS_position 
Protein_position        Amino_acids     Codons Existing_variation      Extra
.       tig00000004_pilon_pilon:232205  A       -       - - 
*intergenic_variant*      -       -       - -       -       -       
IMPACT=MODIFIER
variant_effect_output.txt (END)


It does not work, it retreives only integenic variants which is wrong as 
I have some SNPs in genes...

When I try the tools on data that I used to work on using gtf2vep.pl a 
few years ago, it does not work either....

Could you please help me and tell me if I am doing something wrong?

Thank you in advance.

Best regards,

Sabrina
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Sabrina

	

**Sabrina LEGOUEIX RODRIGUEZ**
Responsable Plateau Bioinformatique

Tél. : +33 (0) 5 61 28 57 92
sabrina.legoueix at toulouse.inra.fr <mailto:[MAIL]>
www.toulouse-white-biotechnology.com 
<http://www.toulouse-white-biotechnology.com/>

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