ensembl VEP variant not annotated

Question

[cocchi.e89]

I am working with some variants and try to annotate them with VEP, I have noticed that some variants (as example 1-2866128-C-T on chr 1) are not annotated by VEP, my output (VCF format):

1   2866128 .   C   T   .   .   .

my command:

  ./vep \
    -i "$file_inputed" \
    --cache  --dir_cache /Volumes/enricoWD/vep/vep_cache/ \
    --fasta /Volumes/enricoWD/vep/vep_fasta/homo_sapiens/96_GRCh37/Homo_sapiens.GRCh37.dna.primary_assembly.fa \
    --dir_plugins /Volumes/enricoWD/vep/vep_plugins/ \
    --hgvs \
    --no_stats \
    --offline  \
    --symbol \
    --vcf \
    --pick_allele_gene \
    --no_intergenic \
    --gencode_basic \
    --sift b \
    --polyphen b \
    --plugin dbNSFP,/Volumes/enricoWD/dbNFSP/v4.0/dbNSFP_hg19.gz,LRT_score,LRT_pred,GERP++_RS \
    --plugin dbscSNV,/Volumes/enricoWD/dbNFSP/dbsc/dbscSNV1.1_GRCh37.txt.gz \
    --assembly GRCh37 \
    -o "$file_outputed" 2>&1 >> "$log_file"

Does anybody got a clue? And in such case how could I retrieve the variant effect for those variants?

Thanks a lot in advance for any help!

Answer 1

[Pierre Lindenbaum]

for 1:2866128 as far as I can see it's intergenic, while --no_intergenic is set...