[ensembl-dev] ClinVar Review Status

[Sarah Hunt]

Hi Michael,

The ClinVar ReviewStatus isn't available in the cache, but can be 
accessed using the Phenotypes plugin:

https://github.com/Ensembl/VEP_plugins/blob/release/93/Phenotypes.pm

This returns all attributes for all phenotypes with optional filtering 
by data source. It is only available when using json output format 
currently as each variant can return a large amount of data which 
doesn't fit well in VCF. We could extend the filtering and enable small 
numbers of attributes to be added to VCF.

Best wishes,

Sarah

On 11/08/2018 18:26, Michael Yourshaw wrote:
> VEP provides the annotation CLIN_SIG : ClinVar clinical significance 
> of the dbSNP variant
>
> Is there a direct way to get the ClinVar ReviewStatus from VEP?
>
> If not, is ClinVar ReviewStatus available somewhere in the VEP 
> cache/database so that it could easily be retreived with a VEP plugin?
>
>
>
> ॐ
> Michael Yourshaw
> myourshaw at gmail.com <mailto:myourshaw at ucla.edu>
>
> This message is intended only for the use of the addressee and may 
> contain information that is PRIVILEGED and CONFIDENTIAL, and/or may 
> contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, 
> you are hereby notified that any dissemination of this communication 
> is strictly prohibited. If you have received this communication in 
> error, please erase all copies of the message and its attachments and 
> notify us immediately. Thank you.
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20180813/86fb8fc1/attachment.html>