MITOMAP annotations support, Splice Junction Tracks and maintenance

[4.32]

Added

• Load and show MITOMAP associated diseases from VCF (INFO field: MitomapAssociatedDiseases, via HmtNote)
• Show variant allele frequencies for mitochondrial variants (GRCh38 cases)
• Extend "public" json API with diseases (OMIM) and phenotypes (HPO)
• HPO gene list download now has option for clinical and non-clinical genes
• Display gene splice junctions data in sashimi plots
• Update case individuals with splice junctions tracks
• Simple Docker compose for development with local build
• Make Phenomodels subpanels collapsible
• User side documentation of cytogenomics features (Gens, Chromograph, vcf2cytosure, rhocall)
• iSort GitHub Action

Fixed

• Show other causative once, even if several events point to it
• Filtering variants by mitochondrial chromosome for cases with genome build=38
• HPO gene search button triggers any warnings for clinical / non-existing genes also on first search
• Fixed a bug in variants pages caused by MT variants without alt_frequency
• Tests for CADD score parsing function
• Fixed the look of IGV settings on SNV variant page
• Cases analyzed once shown as rerun
• Missing case track on case re-upload
• Fixed severity rank for SO term "regulatory region ablation"

Changed

• Refactor according to CodeFactor - mostly reuse of duplicated code
• Phenomodels language adjustment
• Open variants in a new window (from variants page)
• Open overlapping and compound variants in a new window (from variant page)
• gnomAD link points to gnomAD v.3 (build GRCh38) for mitochondrial variants.
• Display only number of affected genes for dismissed SVs in general report
• Chromosome build check when populating the variants filter chromosome selection
• Display mitochondrial and rare diseases coverage report in cases with missing 'rare' track

Cancer-specific case reports and ClinVar form fix

[4.31.1]

Added

Changed

• Remove mitochondrial and coverage report from cancer cases sidebar

Fixed

• ClinVar page when dbSNP id is None

New documentation links and continuous maintenance

[4.31]

Added

• gnomAD annotation field in admin guide
• Export also dynamic panel genes not associated to an HPO term when downloading the HPO panel
• Primary HGNC transcript info in variant export files
• Show variant quality (QUAL field from vcf) in the variant summary
• Load/update PDF gene fusion reports (clinical and research) generated with Arriba
• Support new MANE annotations from VEP (both MANE Select and MANE Plus Clinical)
• Display on case activity the event of a user resetting all dismissed variants
• Support gnomAD population frequencies for mitochondrial variants
• Anchor links in Casedata ClinVar panels to redirect after renaming individuals

Fixed

• Replace old docs link www.clinicalgenomics.se/scout with new https://clinical-genomics.github.io/scout
• Page formatting issues whenever case and variant comments contain extremely long strings with no spaces
• Chromograph images can be one column and have scrollbar. Removed legacy code.
• Column labels for ClinVar case submission
• Page crashing looking for LoqusDB observation when variant doesn't exist
• Missing inheritance models and custom inheritance models on newly created gene panels
• Accept only numbers in managed variants filter as position and end coordinates
• SNP id format and links in Variant page, ClinVar submission form and general report
• Case groups tooltip triggered only when mouse is on the panel header

Changed

• A more compact case groups panel
• Added landscape orientation CSS style to cancer coverage and QC demo report
• Improve user documentation to create and save new gene panels
• Removed option to use space as separator when uploading gene panels
• Separating the columns of standard and custom inheritance models in gene panels
• Improved ClinVar instructions for users using non-English Excel

Fix and empty VEP RefSeq IDS and bug in server/links

[4.30.2]

Added

Fixed

• Use VEP RefSeq ID if RefSeq list is empty in RefSeq transcripts overview
• Bug creating variant links for variants with no end_chrom

Changed

Fix broken cryptography dependency

[4.30.1]

Added

Fixed

• Cryptography dependency fixed to use version < 3.4

Changed

Gens integration and visualization of all alignments of a case group

[4.30]

Added

• Introduced a reset dismiss variant verb
• Button to reset all dismissed variants for a case
• Add black border to Chromograph ideograms
• Show ClinVar annotations on variantS page
• Added integration with GENS, copy number visualization tool
• Added a VUS label to the manual classification variant tags
• Add additional information to SNV verification emails
• Tooltips documenting manual annotations from default panels
• Case groups now show bam files from all cases on align view

Fixed

• Center initial igv view on variant start with SNV/indels
• Don't set initial igv view to negative coordinates
• Display of GQ for SV and STR
• Parsing of AD and related info for STRs
• LoqusDB field in institute settings accepts only existing Loqus instances
• Fix DECIPHER link to work after DECIPHER migrated to GRCh38
• Removed visibility window param from igv.js genes track
• Updated HPO download URL
• Patch HPO download test correctly
• Reference size on STR hover not needed (also wrong)
• Introduced genome build check (allowed values: 37, 38, "37", "38") on case load
• Improve case searching by assignee full name
• Populating the LoqusDB select in institute settings

Changed

• Cancer variants table header (pop freq etc)
• Only admin users can modify LoqusDB instance in Institute settings
• Style of case synopsis, variants and case comments
• Switched to igv.js 2.7.5
• Do not choke if case is missing research variants when research requested
• Improve create new gene panel form validation
• Make XM- transcripts less visible if they don't overlap with transcript refseq_id in variant page
• Color of gene panels and comments panels on cases and variant pages

v4.29.1

[4.29.1]

Added

Fixed

• Always load STR variants regardless of RankScore threshold (hotfix)

Changed

STRs filtering, cancer QC and coverage report and igv.js browser fixes

[4.29]

Added

• Added a page about migrating potentially breaking changes to the documentation
• markdown_include in development requirements file
• STR variants filter
• Display source, Z-score, inheritance pattern for STR annotations from Stranger (>0.6.1) if available
• Coverage and quality report to cancer view

Fixed

• ACMG classification page crashing when trying to visualize a classification that was removed
• Pretty print HGVS on gene variants (URL-decode VEP)
• Broken or missing link in the documentation
• Multiple gene names in ClinVar submission form
• Inheritance model select field in ClinVar submission
• IGV.js >2.7.0 has an issue with the gene track zoom levels - temp freeze at 2.7.0
• Revert CORS-anywhere and introduce a local http proxy for cloud tracks

Chromograph and Beacon integration. Container deployment files

[4.28]

Added

• Chromograph integration for displaying PNGs in case-page
• Add VAF to cancer case general report, and remove some of its unused fields
• Variants filter compatible with genome browser location strings
• Support for custom public igv tracks stored on the cloud
• Add tests to increase testing coverage
• Update case variants count after deleting variants
• Update IGV.js to latest (v2.7.4)
• Bypass igv.js CORS check using https://github.com/Rob--W/cors-anywhere
• Documentation on default and custom IGV.js tracks (admin docs)
• Lock phenomodels so they're editable by admins only
• Small case group assessment sharing
• Tutorial and files for deploying app on containers (Kubernetes pods)
• Canonical transcript and protein change of canonical transcript in exported variants excel sheet
• Support for Font Awesome version 6
• Submit to Beacon from case page sidebar
• Hide dismissed variants in variants pages and variants export function
• Systemd service files and instruction to deploy Scout using podman

Fixed

• Bugfix: unused chromgraph_prefix |tojson removed
• Freeze coloredlogs temporarily
• Marrvel link
• Don't show TP53 link for silent or synonymous changes
• OMIM gene field accepts any custom number as OMIM gene
• Fix Pytest single quote vs double quote string
• Bug in gene variants search by similar cases and no similar case is found
• Delete unused file userpanel.py
• Primary transcripts in variant overview and general report
• Google OAuth2 login setup in README file
• Redirect to 'missing file'-icon if configured Chromograph file is missing
• Javascript error in case page
• Fix compound matching during variant loading for hg38
• Cancer variants view containing variants dismissed with cancer-specific reasons
• Zoom to SV variant length was missing IGV contig select
• Tooltips on case page when case has no default gene panels

Changed

• Save case variants count in case document and not in sessions
• Style of gene panels multiselect on case page
• Collapse/expand main HPO checkboxes in phenomodel preview
• Replaced GQ (Genotype quality) with VAF (Variant allele frequency) in cancer variants GT table
• Allow loading of cancer cases with no tumor_purity field
• Truncate cDNA and protein changes in case report if longer than 20 characters

Option to remove variants by category

[4.27]

Added

• Exclude one or more variant categories when running variants delete command

Fixed

Changed