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

David Blaney David.Blaney at ogt.com
Wed May 13 14:24:04 BST 2015

Thanks for that Will,

I thought this might have been the case for this variant, but let’s say we have a variant that is co-located with a ‘passed QC’  (same allele)  dbSNP variant and a HGMD variant.

My understanding is that VEP (with –check-existing, --check-alleles) would report the co-located variant but not the HGMD variant because it cannot check the HGMD allele. Is it possible to overwrite the check allele for HGMD (or sources that have no allele information) and hence report both the matched allele dbSNP and HGMD entry? I understand that –check-alleles is only doing its job.

Here is an example, VEP (--check-existing & --check-alleles):


VEP (--check-existing only):



From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 13 May 2015 11:28
To: Ensembl developers list
Subject: Re: [ensembl-dev] HDMG/dbSNP co-located variants

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).


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


Will McLaren
Ensembl Variation

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


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:


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?


Many thanks in advance,

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