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Improved cancer case pages, new features and bugfixes

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@northwestwitch northwestwitch released this 20 Aug 09:28
v4.37
d0f9383
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Learn about vigilant mode.

[4.37]

Added

  • Highlight and show version number for RefSeq MANE transcripts.
  • Added integration to a rerunner service for toggling reanalysis with updated pedigree information
  • SpliceAI display and parsing from VEP CSQ
  • Display matching tiered variants for cancer variants
  • Display a loading icon (spinner) until the page loads completely
  • Display filter badges in cancer variants list
  • Update genes from pre-downloaded file resources
  • On login, OS, browser version and screen size are saved anonymously to understand how users are using Scout
  • API returning institutes data for a given user: /api/v1/institutes
  • API returning case data for a given institute: /api/v1/institutes/<institute_id>/cases
  • Added GMS and Lund university hospital logos to login page
  • Made display of Swedac logo configurable
  • Support for displaying custom images in case view
  • Individual-specific HPO terms
  • Optional alamut_key in institute settings for Alamut Plus software
  • Case report API endpoint
  • Tooltip in case explaining that genes with genome build different than case genome build will not be added to dynamic HPO panel.
  • Add DeepVariant as a caller

Fixed

  • Updated IGV to v2.8.5 to solve missing gene labels on some zoom levels
  • Demo cancer case config file to load somatic SNVs and SVs only.
  • Expand list of refseq trancripts in ClinVar submission form
  • Renamed All SNVs and INDELs institute sidebar element to Search SNVs and INDELs and fixed its style.
  • Add missing parameters to case load-config documentation
  • Allow creating/editing gene panels and dynamic gene panels with genes present in genome build 38
  • Bugfix broken Pytests
  • Bulk dismissing variants error due to key conversion from string to integer
  • Fix typo in index documentation
  • Fixed crash in institute settings page if "collaborators" key is not set in database
  • Don't stop Scout execution if LoqusDB call fails and print stacktrace to log
  • Bug when case contains custom images with value None
  • Bug introduced when fixing another bug in Scout-LoqusDB interaction
  • Loading of OMIM diagnoses in Scout demo instance
  • Remove the docker-compose with chanjo integration because it doesn't work yet.
  • Fixed standard docker-compose with scout demo data and database
  • Clinical variant assessments not present for pinned and causative variants on case page.
  • MatchMaker matching one node at the time only
  • Remove link from previously tiered variants badge in cancer variants page
  • Typo in gene cell on cancer variants page
  • Managed variants filter form

Changed

  • Better naming for variants buttons on cancer track (somatic, germline). Also show cancer research button if available.
  • Load case with missing panels in config files, but show warning.
  • Changing the (Female, Male) symbols to (F/M) letters in individuals_table and case-sma.
  • Print stacktrace if case load command fails
  • Added sort icon and a pointer to the cursor to all tables with sortable fields
  • Moved variant, gene and panel info from the basic pane to summary panel for all variants.
  • Renamed Basics panel to Classify on variant page.
  • Revamped Basics panel to a panel dedicated to classify variants
  • Revamped the summary panel to be more compact.
  • Added dedicated template for cancer variants
  • Removed Gene models, Gene annotations and Conservation panels for cancer variants
  • Reorganized the orders of panels for variant and cancer variant views
  • Added dedicated variant quality panel and removed relevant panes
  • A more compact case page
  • Removed OMIM genes panel
  • Make genes panel, pinned variants panel, causative variants panel and ClinVar panel scrollable on case page
  • Update to Scilifelab's 2020 logo
  • Update Gens URL to support Gens v2.0 format
  • Refactor tests for parsing case configurations
  • Updated links to HPO downloadable resources
  • Managed variants filtering defaults to all variant categories
  • Changing the (Kind) drop-down according to (Category) drop-down in Managed variant add variant
  • Moved Gens button to individuals table
  • Check resource files availability before starting updating OMIM diagnoses
  • Fix typo in SHOW_OBSERVED_VARIANT_ARCHIVE config param
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