[ensembl-dev] VEP doesn't display 'SYMBOL' when Feature is "NM_*"

Pierre Lindenbaum pierre.lindenbaum at univ-nantes.fr
Tue Jan 26 10:49:13 GMT 2016


Hi Ensembl  :-)

I'm running vep 83 on my VCF,

(...)/vep/ensembl-tools-release-83/scripts/variant_effect_predictor/variant_effect_predictor.pl 
--cache --dir ${vep.cache} --write_cache                 --species 
homo_sapiens_merged           --assembly  GRCh37 --db_version 
83            --fasta $(REF) --offline               --symbol --protein 
--canonical --biotype                --fork 10               --format 
vcf --vcf         --force_overwrite                --numbers 
--total_length --terms so             --xref_refseq           -o stdout 
--no_stats

It seems that each time a Feature is an (NM_* , XM_* = entry, VEP 
doesn't display the SYMBOL. (See an example below: SYMBOL should be 
'MTOR' isn't it ?)



         >>> 12
        $1    #CHROM    1
        $2    POS    11249565
        $3    ID    rs142826661
        $4    Allele    A
        $5    Consequence    intron_variant
        $6    IMPACT    MODIFIER
        $7    SYMBOL    .
        $8    Gene    2475
        $9    Feature_type    Transcript
        $10    Feature    NM_004958.3
        $11    BIOTYPE    protein_coding
        $12    EXON    .
        $13    INTRON    28/57
        $14    HGVSc    .
        $15    HGVSp    .
        $16    cDNA_position    -/8725
        $17    CDS_position    -/7650
        $18    Protein_position    -/2549
        $19    Amino_acids    .
        $20    Codons    .
        $21    Existing_variation    .
        $22    DISTANCE    .
        $23    STRAND    -1
        $24    SYMBOL_SOURCE    .
        $25    HGNC_ID    .
        $26    CANONICAL    .
        $27    ENSP    NP_004949.1
        $28    RefSeq    .
        <<< 12


Am I wrong ?
Thank you for your help :-)

Regards,



Pierre Lindenbaum / @yokofakun / INSERM / France












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