[ensembl-dev] VEP output question/bug?

Fiona Cunningham fiona at ebi.ac.uk
Thu Dec 29 14:30:03 GMT 2011

Dear Mark,

The VEP takes your given reference allele as the one to use to
calculate the change. So if you change the input ref allele, the
output changes too. There is a flag to check if your input ref allele
really matches the reference assembly allele if you want that.

Let us know if you wanted a different behaviour here.


Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org || www.lrg-sequence.org
fiona at ebi.ac.uk   || t: +44 1223 494612

On 23 December 2011 20:13, Mark Aquino <aquinom85 at me.com> wrote:
> Hey guys,
> Today I got an output from VEP with 2 different ref alleles at the same site (G and C).
> e.,g.
> chrom  start            allele    gene_id                   transcript_id                                                                                                                      amino_acid   codon
> 7         36429636      A       ENSG00000011426 ENST00000265748 Transcript      NON_SYNONYMOUS_CODING   222     1       1       V/M              Gtg/Atg -       -
> 7         36429636      A       ENSG00000011426 ENST00000265748 Transcript      NON_SYNONYMOUS_CODING   222     1       1       L/M               Ctg/Atg -       -
> Is this a bug, or why are there 2 ref alleles at this same position...?
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