Matching causative IGH::DUX4 not displayed on case page - works from variant page

[dnil]

Describe the bug
Matching causative IGH::DUX4 not displayed on case page - works from variant page

To Reproduce
Steps to reproduce the behavior:

1. Visit a case page for a case with a positive IGH::DUX4, eg sweepingcardinal, as can be seen from its variant page
2. Click matching causatives
3. See error

These panel cases do not have a gene panel. Nor does the BND really. Perhaps something goes awry in separating the in-gene list from outside ones when there is no gene on the variant or no panels on the case.

[northwestwitch]

Ah I think I might know why this happened. There is this step in the search for matching causatives that makes sure that the variant matched in the case is called in the affected sample. The problem with case sweepingcardinal is that genotype is not set in that variant:

So the GT check fails and no matching causatives are returned in the case.

[northwestwitch]

I think we should work on a fix when loading this weird variant in the database then

[dnil]

Ah, we could also pass it back to the pipeline, and just update the IGH-DUX4 script to also write a fake GT? It does intend to say the variant is found in that sample...

[dnil]

Sorry folks, we are a little tired: we can discuss after the Holidays, but for now we drop this on your lap. It would be super nice if the IGH-DUX4 caller just set a GT on the affected sample as well! 😊