Search through all cases

[moonso]

We should think of a solution for how to do searches for all variants in all cases. When using the gemini- and mongo adapters this will be straightforward, we just need to figure out how the interface can handle this.

EDIT: from #213

• [ ] should be able to decide which individuals to include (from multiple cases)

[robinandeer]

Are we still targeting this for the VCF-adapter? Will tabix make this easier?

[moonso]

We can try to do it for the VCF adapter as well. One of the challenging things is how it should be visualized in puzzle. I have limited experience with these kind of analysis so if anyone else have ideas please post them!

[guillermo-carrasco]

I don't :-/ I'll ping @ohofmann just in case he has an idea of how this should be visualized.

[ohofmann]

I don't think we'll be looking for all-variants-in-all-cases regularly. All variants at a given location, maybe (which will rarely be larger than a gene), and that's mostly for context. Could do this via ad hoc aggregation (sum of samples with this mutation, with mutations of a certain impact in this gene, etc.).

[vasiliosz]

@Bianca-T might have some ideas/use cases

[genecracker]

I think it is very useful to have a function for searching all the cases. Would use it for:

• search for mutations in all cases in a specific gene (great if frequency or impact filters could be added to this query); for example whenever a new gene is published in my field of research I currently use a gemini query to look for all variants (with certain characteristics) in my whole database;
• search for a specific variant/mutation in all cases (this could also help identify recurrent false positive variants);

The best would be to have a search bar that can be used a bit like the ExAC browser for gene level, variant level, transcript level, Rs ID level and even region level for e.g. regulatory elements or similar breakpoints area for SV

[moonso]

So is there any idea how we would present the result of such a query?

[genecracker]

I would suggest a summary table with few but relevant info (e.g. the table in the variant page; genomic position, nucleotidic change, gene, effect, etc...), with the addition of the sample that carries the variant and his/her genotype at that specific variant. Even better with a hyperlink to the specific variant page for each case so that further exploring can be done.

Disclaimer: have no idea of harder this implementation can be :smile: