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

[David Blaney]

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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