ensembl VEP variant not annotated
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Entering edit mode
23 months ago
cocchi.e89 ▴ 140

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!

ensembl vep variants annotation • 809 views
3
Entering edit mode
23 months ago

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