[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
-----------------------------------------------------------------------------------
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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