Building DBs for gemini?!!

[alka...@gmail.com]

Thank you for the development of this great tool.

I'm wondering if it is possible to build my own databases that I can just add to the 'gemini_data' folder, and be able to use them as default annotation files.

I have the HGMD, which I currently have to use the 'annotate' extract feature, in order to add it to my file; but I'd like to know if there is a way of adding it to the default data folder of gemini?

I'd also like to upgrade the current gnomAD DB from being only for exomes to the whole genome. How can I curate the downloaded vcf files from the gnomAD website to make it manageable by gemini?

It is mentioned in the paper of gemini that instructions and databases used are available at http://quinlanlab.cs.virginia.edu/ but I'm afraid that this page is not available.

I'd appreciate any help with that, since it is going to make gemini the ultimate one-stop for our analyses.

Best,

[Brent Pedersen]

You'll have to create the database with gemini, or with vcf2db
(https://github.com/quinlan-lab/vcf2db/) in order to use the
annotations.

You can see how to use vcf2db along with your own annotations here:
http://quinlanlab.org/blog/2016/05/02/gemini-2-progress.html
we haven't advertised that too much lately, but there are quite a
number of folks using that loading method.

hope that helps,
-Brent

[alka...@gmail.com]

That was really helpful... Thank you very much!