[ensembl-dev] Question regarding rs#'s - location only vs. location + nucleotide

Will McLaren wm2 at ebi.ac.uk
Wed Jun 24 08:54:12 BST 2015


Hello Mollie,

The VEP can compare the alleles of your input with those from the rs#
variants; select "Yes and compare alleles" from the "Find co-located known
variants:" dropdown menu under the "Identifiers and frequency data" tab
when you submit your job.

In the standalone tool, you must add the "--check_alleles" flag.

Online: http://www.ensembl.org/info/docs/tools/vep/online/input.html#ident
Standalone:
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_check_existing

Regards

Will McLaren
Ensembl Variation

On 23 June 2015 at 20:22, Ullman-Cullere, Mollie <
MULLMANCULLERE at partners.org> wrote:

> The rs# is a location identifier, where theoretically one rs# may have
> multiple variants A/T, A/C, A/G.  To muddy the waters further, you may have
> A/T somatic, A/T germline etc...
>
> I've been testing VEP GRCh 37 (online version) and found the rs# is
> returned on a matching of location and not location + nucleotide change.
> Would you please confirm functionality for both the online and standalone
> tools?
>
> Best regards,
> Mollie
>
> Mollie Ullman-Cullere
> Sr. Clinical Bioinformaticist
> Clinical and Translational Informatics
> Dana-Farber Cancer Institute/Partners Healthcare
>
>
>
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