PanelApp Green genes, ACMG modification links, research variant counting and UI fixes

[4.64]

Added

• Create/Update a gene panel containing all PanelApp green genes (scout update panelapp-green -i <cust_id>)
• Links for ACMG pathogenicity impact modification on the ACMG classification page

Changed

• Open local observation matching cases in new windows

Fixed

• Matching manual ranked variants are now shown also on the somatic variant page
• VarSome links to hg19/GRCh37
• Managed variants filter settings lost when navigating to additional pages
• Collect the right variant category after submitting filter form from research variantS page
• Beacon links are templated and support variants in genome build 38

nf-core-rnafusion reports, modified ACMG, risk factors and ClinVar submission fixes

[4.63]

Added

• Display data sharing info for ClinVar, Matchmaker Exchange and Beacon in a dedicated column on Cases page
• Test for commands.download.omim.print_omim
• Display dismissed variants comments on general case report
• Modify ACMG pathogenicity impact (most commonly PVS1, PS3) based on strength of evidence with lab director's professional judgement
• REViewer button on STR variant page
• Alamut institution parameter in institute settings for Alamut Visual Plus software
• Added Manual Ranks Risk Factor, Likely Risk Factor and Uncertain Risk Factor
• Display matching manual ranks from previous cases the user has access to on VariantS and Variant pages
• Link to gnomAD gene SVs v2.1 for SV variants with gnomAD frequency
• Support for nf-core/rnafusion reports

Changed

• Display chrY for sex unknown
• Deprecate legacy scout_load() method API call.
• Message shown when variant tag is updated for a variant
• When all ACMG classifications are deleted from a variant, the current variant classification status is also reset.
• Refactored the functions that collect causative variants
• Removed scripts/generate_test_data.py

Fixed

• Default IGV tracks (genes, ClinVar, ClinVar CNVs) showing even if user unselects them all
• Freeze Flask-Babel below v3.0 due to issue with a locale decorator
• Thaw Flask-Babel and fix according to v3 standard. Thank you @TkTech!
• Show matching causatives on somatic structural variant page
• Visibility of gene names and functional annotations on Causatives/Verified pages
• Panel version can be manually set to floating point numbers, when modified
• Causatives page showing also non-causative variants matching causatives in other cases
• ClinVar form submission for variants with no selected transcript and HGVS
• Validating and submitting ClinVar objects not containing both Variant and Casedata info

New Contributors

• @fevac made their first contribution in #3747

Full Changelog: v4.62...v4.63

Fix bug in case group feature

[4.62.1]

Fixed

• Case page crashing when adding a case to a group without providing a valid case name

v4.62 - ClinVar API submission, Phenopackets and REViewer fallback

[4.62]

Added

• Validate ClinVar submission objects using the ClinVar API
• Wrote tests for case and variant API endpoints
• Create ClinVar submissions from Scout using the ClinVar API
• Export Phenopacket for affected individual
• Import Phenopacket from JSON file or Phenopacket API backend server
• Use the new case name option for GENS requests
• Pre-validate refseq:HGVS items using VariantValidator in ClinVar submission form

Fixed

• Fallback for empty alignment index for REViewer service
• Source link out for MIP 11.1 reference STR annotation
• Avoid duplicate causatives and pinned variants
• ClinVar clinical significance displays only the ACMG terms when user selects ACMG 2015 as assertion criteria
• Spacing between icon and text on Beacon and MatchMaker links on case page sidebar
• Truncate IDs and HGVS representations in ClinVar pages if longer than 25 characters
• Update ClinVar submission ID form
• Handle connection timeout when sending requests requests to external web services
• Validate any ClinVar submission regardless of its status
• Empty Phenopackets import crashes
• Stop Spinner on Phenopacket JSON download

Changed

• Updated ClinVar submission instructions

Patches to ClinVar submission flow

[4.61.1]

Fixed

• Added UMLS as an option of Condition ID type in ClinVar Variant downloaded files
• Missing value for Condition ID type in ClinVar Variant downloaded files
• Possibility to open, close or delete a ClinVar submission even if it doesn't have an associated name
• Save SV type, ref and alt n. copies to exported ClinVar files
• Inner and outer start and stop SV coordinates not exported in ClinVar files
• ClinVar submissions page crashing when SV files don't contain breakpoint exact coordinates
• Align OMIM diagnoses with delete diagnosis button on case page
• In ClinVar form, reset condition list and customize help when condition ID changes

Version 4.61: ClinVar submission simplified, inheritance model colors, and more custom report types

[4.61]

Added

• Filter case list by cases with variants in ClinVar submission
• Filter case list by cases containing RNA-seq data - gene_fusion_reports and sample-level tracks (splice junctions and RNA coverage)
• Additional case category Ignored, to be used for cases that don't fall in the existing 'inactive', 'archived', 'solved', 'prioritized' categories
• Display number of cases shown / total number of cases available for each category on Cases page
• Moved buttons to modify case status from sidebar to main case page
• Link to Mutalyzer Normalizer tool on variant's transcripts overview to retrieve official HVGS descriptions
• Option to manually load RNA MULTIQC report using the command scout load report -t multiqc_rna
• Load RNA MULTIQC automatically for a case if config file contains the multiqc_rna key/value
• Instructions in admin-guide on how to load case reports via the command line
• Possibility to filter RD variants by a specific genotype call
• Distinct colors for different inheritance models on RD Variant page
• Gene panels PDF export with case variants hits by variant type
• A couple of additional README badges for GitHub stats
• Upload and display of pipeline reference info and executable version yaml files as custom reports
• Testing CLI on hasta in PR template

Changed

• Instructions on how to call dibs on scout-stage server in pull request template
• Deprecated CLI commands scout load <delivery_report, gene_fusion_report, coverage_qc_report, cnv_report> to replace them with command scout load report -t <report type>
• Refactored code to display and download custom case reports
• Do not export Assertion method and Assertion method citation to ClinVar submission files according to changes to ClinVar's submission spreadsheet templates.
• Simplified code to create and download ClinVar CSV files
• Colorize inheritance models badges by category on VariantS page
• Safe variants matching badge more visible on case page

Fixed

• Non-admin users saving institute settings would clear loqusdb instance selection
• Layout of variant position, cytoband and type in SV variant summary
• Broken Build Status - GitHub badge on GitHub README page
• Visibility of text on grey badges in gene panels PDF exports
• Labels for dashboard search controls
• Dark mode visibility for ClinVar submission
• Whitespaces on outdated panel in extent report

Mitosign, disabled rerun emails, safe variant matching and misc fixes

[4.60]

Added

• Mitochondrial deletion signatures (mitosign) can be uploaded and shown with mtDNA report
• A Type of analysis column on Causatives and Validated variants pages
• List of "safe" gene panels available for matching causatives and managed variants in institute settings, to avoid secondary findings
• svdb_origin as a synonym for FOUND_IN to complement set for variants found by all callers

Changed

• Hide removed gene panels by default in panels page
• Removed option for filtering cancer SVs by Tumor and Normal alt AF
• Hide links to coverage report from case dynamic HPO panel if cancer analysis
• Remove rerun emails and redirect users to the analysis order portal instead
• Updated clinical SVs igv.js track (dbVar) and added example of external track from https://trackhubregistry.org/

Fixed

• If trying to load a badly formatted .tsv file an error message is displayed.
• Avoid showing case as rerun when first attempt at case upload failed
• Dynamic autocomplete search not working on phenomodels page
• Callers added to variant when loading case
• Now possible to update managed variant from file without deleting it first
• Missing preselected chromosome when editing a managed variant
• Preselected variant type and subtype when editing a managed variant
• Typo in dbVar ClinVar track, hg19

REViewer-Service integration and improvements

[4.59]

Added

• Button to go directly to HPO SV filter variantS page from case
• Scout-REViewer-Service integration - show REViewer picture if available
• Link to HPO panel coverage overview on Case page
• Specify a confidence threshold (green|amber|red) when loading PanelApp panels
• Functional annotations in variants lists exports (all variants)
• Cancer/Normal VAFs and COSMIC ids in in variants lists exports (cancer variants)

Changed

• Better visualization of regional annotation for long lists of genes in large SVs in Variants tables
• Order of cells in variants tables
• More evident links to gene coverage from Variant page
• Gene panels sorted by display name in the entire Case page
• Round CADD and GnomAD values in variants export files

Fixed

• HPO filter button on SV variantS page
• Spacing between region|function cells in SVs lists
• Labels on gene panel Chanjo report
• Fixed ambiguous duplicated response headers when requesting a BAM file from /static
• Visited color link on gene coverage button (Variant page)

Fix search on Cases and Dashboard

[4.58.1]

Fixed

• Case search with search strings that contain characters that can be escaped

New features and maintenance

[4.58]

Added

• Documentation on how to create/update PanelApp panels
• Add filter by local observations (archive) to structural variants filters
• Add more splicing consequences to SO term definitions
• Search for a specific gene in all gene panels
• Institute settings option to force show all variants on VariantS page for all cases of an institute
• Filter cases by validation pending status
• Link to The Clinical Knowledgebase (CKB) (https://ckb.jax.org/) in cancer variant's page

Fixed

• Added a not-authorized auto-login fixture according to changes in Flask-Login 0.6.2
• Renamed cache_timeout param name of flask.send_file function to max_age (Flask 2.2 compliant)
• Replaced deprecated app.config["JSON_SORT_KEYS"] with app.json.sort_keys in app settings
• Bug in gene variants page (All SNVs and INDELs) when variant gene doesn't have a hgnc id that is found in the database
• Broken export of causatives table
• Query for genes in build 38 on Search SNVs and INDELs page
• Prevent typing special characters ^<>?!=\/ in case search form
• Search matching causatives also among research variants in other cases
• Links to variants in Verified variants page
• Broken filter institute cases by pinned gene
• Better visualization of long lists of genes in large SVs on Causative and Verified Variants page
• Reintroduced missing button to export Causative variants
• Better linking and display of matching causatives and managed variants

Changed

• State that loqusdb observation is in current case if observations count is one and no cases are shown
• Better pagination and number of variants returned by queries in Search SNVs and INDELs page
• Refactored and simplified code used for collecting gene variants for Search SNVs and INDELs page
• Fix sidebar panel icons in Case view
• Fix panel spacing in Case view
• Removed unused database sanger_ordered and case_id,category,rank_score indexes (variant collection)
• Verified variants displayed in a dedicated page reachable from institute sidebar
• Unified stats in dashboard page
• Improved gene info for large SVs and cancer SVs
• Remove the unused variant.str_variant endpoint from variant views
• Easier editing of HPO gene panel on case page
• Assign phenotype panel less cramped on Case page
• Causatives and Verified variants pages to use the same template macro
• Allow hyphens in panel names