identify disease variants using annuvar

[carolW]

Hi,
How to keep the variants that are related to a specific disease such as a specific cancer type when one excludes variants in a vcf file using annovar? Is it possible to identify variants related to a specific disease as there is no annotation in the hg19_snp137.txt for ex?

Look forward to your reply,

Carol

[ak352]

Hi Carol,
You could use OMIM annotations as a first approximation.

Previously you could directly download OMIM using ANNOVAR. But now you have to download it separately. See details here.


But I would highly recommend you to use any other specialised curated database for the specific disease if available because it says here -

As advised by UCSC, the results "should be treated with skepticism and any conclusions based on them should be carefully scrutinized using independent resources", including manual inspection of primary literature.

[Knaus]

Hey Carol,

you could try GeneTalk . It is a crowed curated knowledge base with more than 500 users and groing where all the users can leave annotations on disease causing variants, rate them and filter them with intuitive filtering tools.
Set up a free account at www.gene-talk.de/logins/sign_up and upload VCF files onto your account. The data will be availible and accessible only by you, but you can share it with your colleauges if you would like to do collaborations.

GeneTalk was mentioned in several publications and was especially designed for clinicians and scientists who are in need of a simple platform for variant analysis.