[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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