[ensembl-dev] HDMG/dbSNP co-located variants

[Will McLaren]

Hi David,

The dbSNP variant in question has been flagged by our QC pipeline as failed
(actually in this case by dbSNP; we also include their QC flags).

http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?v=rs55796947

Flagged variants are not included in the VEP output by default; to include
them, add "--failed 1" to your command line.

Regards

Will McLaren
Ensembl Variation

On 11 May 2015 at 12:39, David Blaney <David.Blaney at ogt.com> wrote:

> Dear ensembl developers,
>
>
>
> I am trying to annotate the following variant using the GRCh37 online VEP
> tools and have a couple of questions regarding the ‘Existing Variation’
> column.
>
>
>
> 17 21204210 21204210 C/T
>
>
>
> When I run VEP using the with the defaults parameters (in particular with
> the –check-existing  flag selected and the –check-alleles flag not
> selected) there is a HGMD identifier in the ‘Exisitng Variation’ column
> which is great! Please see the ticket here:
>
>
>
> http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=xasvH54pdz3W0DvS
>
>
>
> When I run VEP using the with the parameters  –check-existing  flag
> selected and the –check-alleles flag selected, there is no ‘Existing
> Variation’ reported, despite the fact that the variant is co-located with a
> dbSNP variant that has the correct alleles. Ticket here:
>
>
>
> http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=s8tIqV5q7NEtd4wV
>
>
>
> I understand that it is not possible to match the allele for HDMG as you
> do not have that information but is there a way I can configure VEP to
> report both HGMD ID and the co-located, matched allele, dbSNP variant.
>
>
>
> An answer to a previous question suggests that this is possible. Could you
> please advise?
>
>
>
> http://lists.ensembl.org/pipermail/dev/2011-May/006173.html
>
>
>
> Many thanks in advance,
>
> David
>
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