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

[Will McLaren]

Hi Pierre,

I'm afraid the gene symbols are missing in the GRCh37 RefSeq and merged
data sets; this is due to a change in the way the data are mapped within
the Ensembl databases.

We are looking into a way to solve this reliably for the next release.

Regards

Will McLaren
Ensembl Variation

On 26 January 2016 at 10:49, Pierre Lindenbaum <
pierre.lindenbaum at univ-nantes.fr> wrote:

> 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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