Releases: Clinical-Genomics/scout
Releases · Clinical-Genomics/scout
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
v4.72.2 - patch it while you can
We have patched the problems that occurred with parsing the updated OMIM files in the 4.72 release, sped up and reduced the memory footprint for the case, caseS and disease_terms.
We also introduce a few small frontend changes; increasing the download limit for STR variants to the same number as other ones, parenthood check fails are more obvious in red, and large numbers with thin spaces don't split across lines so easily.
[4.72.2]
Changed
- A gunicorn maxrequests parameter for Docker server image - default to 1200
- STR export limit increased to 500, as for other variants
- Prevent long number wrapping and use thin spaces for separation, as per standards from SI, NIST, IUPAC, BIPM.
- Speed up case retrieval and lower memory use by projecting case queries
- Make relatedness check fails stand out a little more to new users
- Speed up case retrieval and lower memory use by projecting case queries
- Speed up variant pages by projecting only the necessary keys in disease collection query
Fixed
- Huge memory use caused by cases and variants pages pulling complete disease documents from DB
- Do not include genes fetched from HPO terms when loading diseases
- Consider the renamed fields
Approved Symbol
->Approved Gene Symbol
andGene Symbols
->Gene/Locus And Other Related Symbols
when parsing OMIM terms from genemap2.txt file