[ensembl-dev] Fwd: Custom annotation with vep

[Miguel Perez-Enciso]

Dear developers
I am trying to use variant_effect_predictor.pl with a custom gtf file, I run these commands below but it seems that, although it reads my gtf file, it does not recognize the genes and returns all intergenic variants. I attach also the first rows of my gff file. I have installed latest v. (73). Could you help? Thanks a lot!
Miguel Perez Enciso

sort -k1,1 -k4,4n -k5,5n GFF_NDJ_TR.gtf | bgzip > GFF_NDJ_TR.gtf.gz
tabix -p gff GFF_NDJ_TR.gtf.gz

file=in.vcf

perl variant_effect_predictor.pl --custom GFF_NDJ_TR.gtf.gz,myFeatures,gff,overlap,0 -i $file --species sus_scrofa -o $file.annot --format vcf   --offline --force_overwrite --cache

# gtf file
1       protein_coding  stop_codon      21476516 21476514        .       -       .       gene_id GRM1-201
1       protein_coding  exon    21477448        21476379 .       -      .       gene_id GRM1-201
1       protein_coding  CDS     21477448        21476517 .       -   .       gene_id GRM1-201

...

The first lines of annot  file are ( so it does read my annotation file)

## ENSEMBL VARIANT EFFECT PREDICTOR v73
## Output produced at 2013-09-17 22:04:13
## Connected to
## Using cache in /home/miguel/.vep/sus_scrofa/73
## Using API version 73, DB version ?
## Extra column keys:
## DISTANCE : Shortest distance from variant to transcript
## myFeatures : /home/miguel/Documents/ngs/GFF_NDJ_TR.gtf.gz (overlap)
#Uploaded_variation     Location        Allele  Gene    Feature Feature_type    Consequence     cDNA_position   CDS_position    Protein_position        Amino_acids Codons  Existing_variation      Extra
5_63894199_C/T  5:63894199      T       -       -       -       intergenic_variant      -       -       -       -       -       -