Case / control and custom annotations

[viv-1]

Hi,

I just tested your application and I am really impressed with its efficiency :+1: But there is some limitations that prevent me from using it in production. Some important features are missing :

• Case / control filtering
• Custom annotation

Are you planning to add this kind of features ?

[jdelafon]

Hi, Thanks, I'm glad you like it!

The "case-control filtering" in Varapp is the notion of "affected" and "not affected" individuals that is read from the family pedigree and can be used with genotype filters. You can add as many "control" individuals as you want that are not part of a family and just mark them as "not affected". You can also work with no notion of family and only affected/non-affected samples. There is no plan to add more than this, as it proved to be largely satisfactory for our user base.

Since we use Gemini (or more precisely, Varapp reads data formatted like the sqlite dbs that Gemini produces), you can add custom data with VEP and it will be used by Gemini, too. To have this custom annotation available in your Varapp instance then, it will require very few changes to the code that I could guide you through.

• Adding simple annotation columns to the table is rather straightforward.
• Adding new filters is more intricate (because of the cache) and would require a bit more guidance.
• There is no plan to add a "custom annotation loader".

Varapp is built to filter variants efficiently, not to annotate them. We think that it is easy enough to filter until you get a handful of variants, then (export and) complete the annotation.

[viv-1]

Thanks for your answer.

For case / control, dominant filter can partially fill our need. But sometime we need something more flexible than "variants present in all affected individuals and absent in not affected". For example in one of our project we have 200 case and 200 control for a multi-factorial disease. In this case we need to keep variants that are in a certain proportion of our case (e.g. 90%) and not in our control.

I understand that you don't want to change your software if your users are already satisfied.

I am going to search for another solution. But maybe I will fork your project to make it correspond to our needs.

Thank you for your time and your work. :clap: