clinical-genomics / cgbeacon Goto Github PK

Use a test vcf file and gene panel to check that everything works fine.

And TADAAAA': it's written in python. So the java server we are using is outdated and we should switch to the latest. More info to come!

Tried to re-create the issue you told me about. But installing cgbeacon on a clean environment with python 3.6 works fine and I get not errors. Could you post here the error message @patrikgrenfeldt ?

The beacon size from the service page: https://beacon.scilifelab.se/elixirbeacon/v03/beacon/ doesn't change after adding or removing samples. It doesn't reflect the real number of variants in the database because the elixir service doesn't count the actual variants but refers to the size field in the dataset table.

I have developed a flask web interface to our beacon that is ready to be used, but I think it would be nice to add our beacon under the list of our apps : https://clinical.scilifelab.se/apps. But I've just realized that cgweb is developed in Vue.js. It shouldn't be that difficult to add the beacon interface since a beacon query is a fairly easy task, but I don't have any knowledge of Vue.js, so it would take some time to implement it. Does anybody in our team know Vue.js and have time to help?

To be used in combination with cg @ clinicalgenomics

It doesn't take into account the variants not inserted because they're there from previous samples

Variants with Qual<=20 ---> Variants excluded because of quality

After cgbeacon is in production