Releases: Clinical-Genomics/scout
Releases · Clinical-Genomics/scout
More ORPHA-related refactoring, other improvements and fixes
[4.79]
Added
- Added tags for Sniffles and CNVpytor, two LRS SV callers
- Button on case page for displaying STR variants occurring in the dynamic HPO panel
- Display functional annotation relative to variant gene's MANE transcripts on variant summary, when available
- Links to ACMG structural variant pathogenicity classification guidelines
- Phenomodels checkboxes can now include orpha terms
- Add incidental finding to case tags
Changed
- In the diagnoses page genes associated with a disease are displayed using hgnc symbol instead of hgnc id
- Refactor view route to allow navigation directly to unique variant document id, improve permissions check
- Do not show MANE and MANE Plus Clinical transcripts annotated from VEP (saved in variants) but collect this info from the transcripts database collection
- Refactor view route to allow navigation directly to unique case id (in particular for gens)
Institutes to share cases with
on institute's settings page now displays institutes names and IDs- View route with document id selects view template based on variant category
Fixed
- Refactored code in cases blueprints and variant_events adapter (set diseases for partial causative variants) to use "disease" instead of "omim" to encompass also ORPHA terms
- Refactored code in
scout/parse/omim.py
andscout/parse/disease_terms.py
to use "disease" instead of "phenotype" to differentiate from HPO terms - Be more careful about checking access to variant on API access
- Show also ACMG VUS on general report (could be missing if not e.g. pinned)
Case status labels, ORPHA disorders, MANE and ClinVar updates
[4.78]
Added
- Case status labels can be added, giving more finegrained details on a solved status (provisional, diagnostic, carrier, UPD, SMN, ...)
- New SO terms:
sequence_variant
andcoding_transcript_variant
- More MEI specific annotation is shown on the variant page
- Parse and save MANE transcripts info when updating genes in build 38
Mane Select
andMane Plus Clinical
badges on Gene page, when available- ClinVar submission can now be downloaded as a json file
- API endpoint to pin variant
- Display common/uncommon/rare on summary of mei variant page
Changed
- In the ClinVar form, database and id of assertion criteria citation are now separate inputs
- Customise institute settings to be able to display all cases with a certain status on cases page (admin users)
- Renamed
Clinical Significance
toGermline Classification
on multistep ClinVar form - Changed the "x" in cases.utils.remove_form button text to red for better visibility in dark mode
- Update GitHub actions
- Default loglevel up to INFO, making logs with default start easier to read
- Add XTR region to PAR region definition
- Diagnoses can be searched on diagnoses page without waiting for load first
Fixed
- Removed log info showing hgnc IDs used in variantS search
- Maintain Matchmaker Exchange and Beacon submission status when a case is re-uploaded
- Inheritance mode from ORPHA should not be confounded with the OMIM inheritance model
- Decipher link URL changes
- Refactored code in cases blueprints to use "disease" instead of "omim" to encompass also ORPHA terms
Updates to ClinVar submission, GnomAD constraints, ORPHA and bug fixes
[4.77]
Added
- Orpha disease terms now include information on inheritance
- Case loading via .yaml config file accepts subject_id and phenotype_groups (if previously defined as constant default or added per institute)
- Possibility to submit variants associated with Orphanet conditions to ClinVar
- Option update path to .d4 files path for individuals of an existing case using the command line
- More constraint information is displayed per gene in addition to pLi: missense and LoF OE, CI (inluding LOEUF) and Z-score.
Changed
- Introduce validation in the ClinVar multistep form to make sure users provide at least one variant-associated condition
- CLI scout update individual accepts subject_id
- Update ClinVar inheritance models to reflect changes in ClinVar submission API
- Handle variant-associated condition ID format in background when creating ClinVar submissions
- Replace the code that downloads Ensembl genes, transcripts and exons with the Schug web app
- Add more info to error log when transcript variant frequency parsing fails.
- GnomAD v4 constraint information replaces ExAC constraints (pLi).
Fixed
- Text input of associated condition in ClinVar form now aligns to the left
- Alignment of contents in the case report has been updated
- Missing number of phenotypes and genes from case diagnoses
- Associate OMIM and/or ORPHA diagnoses with partial causatives
- Visualization of partial causatives' diagnoses on case page: style and links
- Revert style of pinned variants window on the case page
- Rename
Clinical significanc
toGermline classification
in ClinVar submissions exported files - Rename
Clinical significance citations
toClassification citations
in ClinVar submissions exported files - Rename
Comment on clinical significance
toComment on classification
in ClinVar submissions exported files - Show matching partial causatives on variant page
- Matching causatives shown on case page consisting only of variant matching the default panels of the case - bug introduced since scout v4.72 (Oct 18, 2023)
- Missing somatic variant read depth leading to report division by zero
d4 files, ClinVar event audit, and winter bug fixes
[4.76]
Added
- Pydantic validation of image paths provided in case load config file
- Info on the user which created a ClinVar submission, when available
- Associate .d4 files to case individuals when loading a case via config file
Changed
- In diagnoses page the load of diseases are initiated by clicking a button
- Revel score, Revel rank score and SpliceAI values are also displayed in Causatives and Validated variants tables
- Remove unused functions and tests
- Analysis type and direct link from cases list for OGM cases
- Removed unused
case_obj
parameter from server/blueprints/variant/controllers/observations function - Possibility to reset ClinVar submission ID
- Allow ClinVar submissions with custom API key for users registered as ClinVar submitters or when institute doesn't have a preset list of ClinVar submitters
- Ordered event verbs alphabetically and created ClinVar-related user events
- Removed the unused "no-variants" option from the load case command line
Fixed
- All disease_terms have gene HGNC ids as integers when added to the scout database
- Disease_term identifiers are now prefixed with the name of the coding system
- Command line crashing with error when updating a user that doesn't exist
- Thaw coloredlogs - 15.0.1 restores errorhandler issue
- Thaw crypography - current base image and library version allow Docker builds
- Missing delete icons on phenomodels page
- Missing cryptography lib error while running Scout container on an ARM processor
- Round CADD values with many decimals on causatives and validated variants pages
- Dark-mode visibility of some fields on causatives and validated variants pages
- Clinvar submitters would be cleared when unprivileged users saved institute settings page
- Added a default empty string in cases search form to avoid None default value
- Page crashing when user tries to remove the same variant from a ClinVar submission in different browser tabs
- Update more GnomAD links to GnomAD v4 (v38 SNVs, MT vars, STRs)
- Empty cells for RNA fusion variants in Causatives and Verified variants page
- Submenu icons missing from collapsible actionbar
- The collapsible actionbar had some non-collapsing overly long entries
- Cancer observations for SVs not appearing in the variant details view
- Archived local observations not visible on cancer variantS page
- Empty Population Frequency column in the Cancer SV Variants view
- Capital letters in ClinVar events description shown on case page
Display gene panel membership on gene hovers, Fusion variant filters, Alamut link improvements, and more
[4.75]
Added
- Hovertip to gene panel names with associated genes in variant view, when variant covers more than one gene
- Tests for panel to genes
- Download of Orphadata en_product6 and en_product4 from CLI
- Parse and save
database_found
key/values for RNA fusion variants - Added fusion_score, ffpm, split_reads, junction_reads and fusion_caller to the list of filters on RNA fusion variants page
- Renamed the function
get_mei_info
toset_mei_info
to be consistent with the other functions - Fixed removing None key/values from parsed variants
Changed
- Allow use of projections when retrieving gene panels
- Do not save custom images as binary data into case and variant database documents
- Retrieve and display case and variant custom images using image's saved path
- Cases are activated by viewing FSHD and SMA reports
- Split multi-gene SNV variants into single genes when submitting to Matchmaker Exchange
- Alamut links also on the gene level, using transcript and HGVS: better for indels. Keep variant link for missing HGVS
- Thaw WTForms - explicitly coerce form decimal field entries when filters fetched from db
Fixed
- Removed some extra characters from top of general report left over from FontAwsome fix
- Do not save fusion variants-specific key/values in other types of variants
- Alamut link for MT variants in build 38
- Convert RNA fusions variants
tool_hits
andfusion_score
keys from string to numbers - Fix genotype reference and alternative sequencing depths defaulting to -1 when values are 0
- DecimalFields were limited to two decimal places for several forms - lifting restrictions on AF, CADD etc.
Fix BioNano API FSHD report requests, missing icons and load OMIM terms not associated to genes
[4.74.1]
Changed
- Parse and save into database also OMIM terms not associated to genes
Fixed
- BioNano API FSHD report requests are GET in Access 1.8, were POST in 1.7
- Update more FontAwesome icons to avoid Pro icons
- Test if files still exist before attempting to load research variants
Loading of RNA fusion variants, missing icons fix & other
[4.74]
Added
- SNVs and Indels, MEI and str variants genes have links to Decipher
- An
owner + case display name
index for cases database collection - Test and fixtures for RNA fusion case page
- Load and display fusion variants from VCF files as the other variant types
- Option to update case document with path to mei variants (clinical and research)
Changed
- Details on variant type and category for audit filters on case general report
- Enable Gens CN profile button also in somatic case view
- Fix case of analysis type check for Gens analysis button - only show for WGS
Fixed
- loqusdb table no longer has empty row below each loqusid
- MatchMaker submission details page crashing because of change in date format returned by PatientMatcher
- Variant external links buttons style does not change color when visited
- Hide compounds with compounds follow filter for region or function would fail for variants in multiple genes
- Updated FontAwesome version to fix missing icons
Fix loading of cases without display name and other improvements
[4.73]
Added
- Shortcut button for HPO panel MEI variants from case page
- Export managed variants from CLI
Changed
- STRs visualization on case panel to emphasize abnormal repeat count and associated condition
- Removed cytoband column from STRs variant view on case report
- More long integers formatted with thin spaces, and copy to clipboard buttons added
Fixed
- OMIM table is scrollable if higher than 700px on SV page
- Pinned variants validation badge is now red for false positives.
- Case display name defaulting to case ID when
family_name
ordisplay_name
are missing from case upload config file - Expanded menu visible at screen sizes below 1000px now has background color
- The image in ClinVar howto-modal is now responsive
- Clicking on a case in case groups when case was already removed from group in another browser tab
GnomAD default build change
A patch release to correct links to match the new GnomAD v4 release, which changed default build to 38 in their API just in time for ASHG.
[4.72.4]
Changed
- Automatic test mongod version increased to v7
Fixed
- GnomAD now defaults to hg38 - change build 37 links accordingly
Fix cancer cases general report report
[4.72.3]
Fixed
- Somatic general case report small variant table can crash with unclassified variants