Scout: Clinvar - New clinsig values do not have internal representation

[henrikstranneheim]

When loading a case with clinvar annotations from: /home/proj/stage/rare-disease/references/references_9.0/grch37_clinvar_reformated_-20200905-.vcf.gz corrsponding to clinvar file: clinvar_20200905.vcf.gz. Scout yields these warnings:

[northwestwitch]

While trying to fix this, I've realized that this might be a bug that we had from before that is not connected to MIP9, but I'm not sure. We should check some old case with a variant having that ClinVar significance value..

[dnil]

But.. but.. surely someone would have tested it if they switched ClinVar file?

[dnil]

Hm, still, I guess: they may have been rare enough before that one test case did not have them?

[northwestwitch]

I guess so

[henrikstranneheim]

Reuploading case strongbison and vitalmouse progress without any errors! Well done!

[northwestwitch]

@henrikstranneheim do you plan to start using MIP9 in production someday soon? Because we should release a new scout version then!

[henrikstranneheim]

@northwestwitch As in want to deploy asap

[henrikstranneheim]

A new release as soon as possible would be great

[northwestwitch]

@mikaell @elevu @dnil let's have one today. Is there anything else we need to merge before releasing what we already have on master?

[dnil]

While trying to fix this, I've realized that this might be a bug that we had from before that is not connected to MIP9, but I'm not sure. We should check some old case with a variant having that ClinVar significance value..

How about this one? I guess just grep:ing for clinsig and \& in a few vcf from bundles of varying age might give something away?

[dnil]

(And checking regarding release..)

[dnil]

Nah, all PRs are currently feature ones, and not extremely urgent ones, and we are not tracking any serious bugs. I guess the view exons remake might constitute a bug fix, so your call on that one is welcome! Otherwise focusing on MIP9 compatibility (plus the already included like editable comments) sounds like a plan!