<div dir="ltr">Hi Pierre,<div><br></div><div>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.</div><div><br></div><div>We are looking into a way to solve this reliably for the next release.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 26 January 2016 at 10:49, Pierre Lindenbaum <span dir="ltr"><<a href="mailto:pierre.lindenbaum@univ-nantes.fr" target="_blank">pierre.lindenbaum@univ-nantes.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Ensembl :-)<br>
<br>
I'm running vep 83 on my VCF,<br>
<br>
(...)/vep/ensembl-tools-release-83/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> --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<br>
<br>
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 ?)<br>
<br>
<br>
<br>
>>> 12<br>
$1 #CHROM 1<br>
$2 POS 11249565<br>
$3 ID rs142826661<br>
$4 Allele A<br>
$5 Consequence intron_variant<br>
$6 IMPACT MODIFIER<br>
$7 SYMBOL .<br>
$8 Gene 2475<br>
$9 Feature_type Transcript<br>
$10 Feature NM_004958.3<br>
$11 BIOTYPE protein_coding<br>
$12 EXON .<br>
$13 INTRON 28/57<br>
$14 HGVSc .<br>
$15 HGVSp .<br>
$16 cDNA_position -/8725<br>
$17 CDS_position -/7650<br>
$18 Protein_position -/2549<br>
$19 Amino_acids .<br>
$20 Codons .<br>
$21 Existing_variation .<br>
$22 DISTANCE .<br>
$23 STRAND -1<br>
$24 SYMBOL_SOURCE .<br>
$25 HGNC_ID .<br>
$26 CANONICAL .<br>
$27 ENSP NP_004949.1<br>
$28 RefSeq .<br>
<<< 12<br>
<br>
<br>
Am I wrong ?<br>
Thank you for your help :-)<br>
<br>
Regards,<br>
<br>
<br>
<br>
Pierre Lindenbaum / @yokofakun / INSERM / France<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div><br></div>