varfish-server

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[clinvar] Provide API endpoint for Variant Information Transfer

1

We need to export Variant Information including Interpretation from Varfish into a database for bookkeeping and at some point for creation of reports. This process is also currently used to...

xiamaz

**Is your feature request related to a problem? Please describe.** We annotate the files with SHA256 checksums in the phenopackets manifest. However, we do not check them. **Describe the solution...

holtgrewe

**Is your feature request related to a problem? Please describe.** #1141 added support for coverage from ngs-bits using MappingQC. Support for other output is missing. **Describe the solution you'd like**...

holtgrewe

**Describe the bug** In a number of places, we currently have duplicate plugin names, e.g., `cases_import.plugins.{ProjectAppPlugin,BackgroundJobsPlugin}`. This causes confusion when plugins are accessed by name. **To Reproduce** N/A **Expected behavior**...

holtgrewe

**Feature** This is a sub-feature for PEDIA-VarFish integration (#399) Docker-compose version of GestaltMatcher (GM) service with REST API endpoint for sending image (GM) service is available. We can integrate GestaltMatcher...

ahujameg

PEDIA integration into VarFish

2

**Is your feature request related to a problem? Please describe.** This is an improvement to integrate PEDIA into VarFish. PEDIA is an approach for prioritization of exome data by facial...

ahujameg

Expose Case Annotations in varfish API

5

Currently an endpoint for retrieving annotations for an individual case is already exposed in the following endpoint: https://github.com/bihealth/varfish-server/blob/1e956c92aabfc7fee9caaefaec60f0034f5e2cc9/cases/views_api.py#L363 This endpoint currently has no permission_classes set and is not reachable. Expected...

xiamaz

**Is your feature request related to a problem? Please describe.** We expect the files in `varfish/static/js` to not be used any more. **Describe the solution you'd like** Remove them. **Describe...

holtgrewe

Consider using playwright for end-to-end UI tests

4

**Is your feature request related to a problem? Please describe.** We are unhappy about Selenium UI tests. [Playwright](https://playwright.dev/python/docs/intro) appears to be a more modern alternative. **Describe the solution you'd like**...

holtgrewe

**Is your feature request related to a problem? Please describe.** It currently is possible to threshold on frequency but not on scores. **Describe the solution you'd like** We should allow...

holtgrewe