Retrieving information from COSMIC database in an automated way

Question

[bt_cepo]

Hi!

I am performing variant calling and annotation of some cancer samples.

For the moment, I am checking manually the variants with an entry in the COSMIC database and then going to the COSMIC database website to retrieve information associated to that variant.

I am wondering if there is any way to do this automatically. This is, finding a variant, filtering the ones that have COSMIC annotation, and then having relevant information associated to that variant being retrieved and written to a report (for example).

I see that COSMIC has downloadable data available but still I do now know how to create a relationship between my vcfs and those files.

I know this might be a very broad and dumb question but I am starting my bioinfo path, I would appreciate any hints to the right answer so I can start figuring out by myself.

Thanks!!

[mohammadhassanj]

Hi, I think others can easily help you with a real example. So give a real and detailed example of expected inputs and outputs.

Answer 1

[jan.rehker]

Check out ANNOVAR.

It can give you the COSMIC ID based on the genomic variant. It will also annotate it in the INFO field of your vcf file.

It is possible to integrate additional and also self crafted databases in ANNOVAR as long as you match an annotation upon a genomic variant.

This is a general idea and I agree with @mohammadhassanj, details would help.