v4.41.1

version 4.41.1 release

Version 4.38.0

[4.38]

Added

• Option to hide Alamut button in the app config file

Fixed

• Library deprecation warning fixed (insert is deprecated. Use insert_one or insert_many instead)
• Update genes command will not trigger an update of database indices any more
• Missing resources in temporary downloading directory when updating genes using the command line
• Restore previous variant ACMG classification in a scrollable div
• Loading spinner not stopping after downloading PDF case reports and variant list export
• Add extra Alamut links higher up on variant pages
• Improve UX for phenotypes in case page
• Filter and export of STR variants
• Update look of variants page navigation buttons

Changed

Version 4.37.0

[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

Version 4.36.0

[4.36]
Added

Parse and save splice junction tracks from case config file
Tooltip in observations panel, explaining that case variants with no link might be old variants, not uploaded after a case rerun

Fixed

Warning on overwriting variants with same position was no longer shown
Increase the height of the dropdowns to 425px
More indices for the case table as it grows, specifically for causatives queries
Splice junction tracks not centered over variant genes
Total number of research variants count
Update variants stats in case documents every time new variants are loaded
Bug in flashing warning messages when filtering variants

Changed

Clearer warning messages for genes and gene/gene-panels searches in variants filters

Version 4.35.0

[4.35]

Added

• A new index for hgnc_symbol in the hgnc_gene collection
• A Pedigree panel in STR page
• Display Tier I and II variants in case view causatives card for cancer cases

Fixed

• Send partial file data to igv.js when visualizing sashimi plots with splice junction tracks
• Research variants filtering by gene
• Do not attempt to populate annotations for not loaded pinned/causatives
• Add max-height to all dropdowns in filters

Changed

• Switch off non-clinical gene warnings when filtering research variants
• Don't display OMIM disease card in case view for cancer cases
• Refactored Individuals and Causative card in case view for cancer cases
• Update and style STR case report

Version 4.34.0

v4.34.0

Add production dockerfile