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varfish-org / varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research
MIT License
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Allow storing variant query results persistently #322

Open holtgrewe opened 2 years ago

holtgrewe commented 2 years ago

Is your feature request related to a problem? Please describe. It is currently only possible to export variant results as a tabular file for storing them persistently. It would be desirable to be able to store variant results persistently within VarFish. This would allow to freeze variants, besides user annotations, for a case, e.g., at the point of writing a diagnostic report.

Describe the solution you'd like Allow users to store query results in a self-contained way with a title.

Describe alternatives you've considered N/A

Additional context N/A

alexejknaus commented 2 years ago

Is your feature request related to a problem? Please describe. Currently User1 can filter a case_X multiple times (e.g. various filter strategies based on mode of inheritance): example:

  1. Filter_dom
  2. Filter_Rez
  3. Filter_X The queries of these filter approaches are logged, but the results are yet not stored permanently.

Two issues arise from this behavior:

  1. There is no documentation of the filtered results and once databases on which bases filtering results change, teh results change, too.
  2. another User2 opening the same case_X will see the last 3. Filter_X and may miss interesting variants in filter steps 1. or 2.

Describe the solution you'd like

  1. After filtering a user should have the possibility to permanently store filtered results: A button "store results" should be available after the first filter was applied.
  2. A name of the filtered results should be provided by the user.
  3. In Case View a new tab should be created: Filtered Results.
  4. Filtered Results displays a list of all stored filter results sortable by date, user, name, filter parameter
  5. Opening the filtered result "Filter_X.rslt" directs you to filter mode. Here, the user may view the content of the filtered result and annotate variants. Further filtering is prohibited, since the variant list is no longer a result of a query.
  6. The Filter_X.rslt is not a VCF file, but rather behaves like a new case within the same family that cannot be filtered.
  7. The Filter _X.rslt can be downloaded as XLSX