Hotfix v4.108.2 - Fix IGV DNA buttons on case page

[4.108.2]

Fixed

• IGV browser page crashing when clicking on IGV gDNA or IGV mtDNA buttons (#6084)

Hotfix v4.108.1 - Fix Tuple TypeError

[4.108.1]

Fixed

• Fix TypeError by replacing Tuple() instantiation with proper tuple return in VariantHandler (#6082)

MethBat outliers, Mimvir/Gicam scores, long reads seq. badges and more

[4.108]

Added

• Gene-overlapping variants shown also for STRs (#5977)
• Case and variant-specific information on ACMG page and PDF export (#5978)
• Allow bypassing the confirmation prompt for the delete rna command via a new --yes option (#5982)
• Parse phasing information and store on genotype call (#5988)
• Link to GTEx for gene, from gene and variant pages (#5995)
• Parse STRdrop details where available (#5991)
• Incomplete penetrance badge, according to HPO (#6008)
• Support for additional variant scoring systems: MivmirScore, GicamScore (#5970)
• Parse and display MivmirExplanation key/values on variant page, when available (#6011)
• Display inheritance models on structural variantS pages (#6015)
• Analysis types wgs-lr and panel-lr (#6029)
• Option to specify database name for the loqusdb API in the scout config file (#6028)
• Allowing filtering cases by type of analysis (advanced options) (#6045)
• Methylation outliers from LRS MethBat from Nallo as omics variants (#5993)
• An ACMG sandbox link included in the main dropdown, pointing to a blank classification page to be used to test the algorithm (#5983)

Changed

• Institutes are now ordered alphabetically by display name on gene panels search (#5965)
• Display all available individual/sample IDs for a case (display_name, individual_id and subject_id) directly on cases page (#5966)
• Revert search of genes in panels. Now search is NOT limited to user's institutes panels any more (#5974)
• Name for Gens buttons: CN profile to Gens(#5985)
• On variants filters form, sort gene panels alphabetically and mark panels that don't belong to the case's clinical panels with asterisk (#5981)
• External links at the bottom of variant page are now ordered alphabetically (#6024)
• Mivmir score explanations sorted by descending value, from the biggest contributor to the smallest (#6058)
• The ACMG classification documentation now more clearly explains about modifications not in Richards et al (#6065)

Fixed

• Do not try to save an ACMG classification when user provided no criteria (#4962)
• When dismissing variants from variantS page, reloaded page remembers variant selection position (#5969)
• Smaller PDFs exported from ACMG classification page (#5976 and #6054)
• When adding a germline variant to a ClinVar submission, make sure it ends up in a germline submission (#5990)
• Invalid scroll_pos handling in variants view (#5999 and #6022)
• Native type hint of iterable with subtype not compatible with python 3.11 (#6007)
• Error in parsing reduced penetrance from HPO genes to phenotypes (#6004)
• Top left SNVs button on omics outliers page (#6001)
• Omics variants RNA sashimi button locus generation does not follow RNA genome build (#6002)
• HGVSp display encoding on gene-variants (SNV and SVs) page (#6018)
• RefSeq transcripts panel on variant page, which was missing RefSeq ID and links for some transcripts (#6027, #6031)
• Phenotype_terms empty crash on case page (#6034)
• Updated supercharge/mongodb-github-action to v1 (1.12.1) in order to fix automatic tests failing with "client too old → daemon too new" error before even starting (#6043,#6044)
• On Local Observations panels, set number of homozygous observations to 0 and not N/A if Nr obs. is 0 (#6038)
• Color case LR badges (#6050)
• Make sorting of gene panels containing a gene case-insensitive (#6052 and #6056)
• Make sorting of institutes case-insensitive on new user form, dashboard and institute settings (#6061, #6062)
• Cases page crashing due to missing analysis date when a case is loaded using VCF + ped file (#6067)
• Add user dropdown selects visible in dark mode (#6068)
• Fixed links to Ensembl and NCBI transcripts from main Transcripts and Protein panel on variant page (#6041)
• Methbat methylation Uncategorized icon display (#6074)
• General report page timeout when case has dozens of dismissed variants - show only the first 15 (#6035)
• Fixed displaying dismissed MEIs and cancer SVs on general case report (#6077)

Patch to ClinVar Oncogenic submissions page

[4.107.2]

Fixed

• Fix ClinVar Oncogenic submissions page crashing (#5960)

Patching bulk dismiss STR/SV/MEI and matching managed variants foldout

What's Changed

• Fix typo in SVs/STRs dismiss many by @northwestwitch in #5955
• Fix find case matching managed variants by @northwestwitch in #5956
• Fix mei dismiss many by @northwestwitch in #5958
• Patch version 4.107.1 by @dnil in #5957

Full Changelog: v4.107...v4.107.1

Variants load speedup, delete RNA command + other improvements and fixes

[4.107]

Added

• On cases page, print a RNA label whenever WGS or WES cases have associated RNA data (#5886)
• Save and display maintainer/institutes for managed variants (#5890)
• Link to VuTR at the transcript level from the variant page (#5893)
• Filter germline ClinVar submission IDs by ClinVar ID (#5907)
• Link to ACMG classification form on SV page - with warnings (#5891)
• scout delete rna -c <case-id> command to remove all RNA-related data from a case (#5916)
• Chromograph ideograms for hg38 (#5883)

Changed

• A case becomes inactive whenever there is a change to any VCF or RNA-associated file (#5888)
• Enhance variants filters by allowing selection of individual soft filters (#5897)
• On ACMG classification form, move Submit button at the bottom and ClinGen gene links to the top (#5876)
• Search panels by gene only within user’s institutes (#5902)
• A more compact gene panels page with panel search options (#5913)
• Extra space for sequencing type badges on cases page (#5920)
• Support multi-value REVEL scores when parsing each transcript (#5923)
• Update GitHub workflows (#5935)
• IGV.js to version 3.7.1 (#5931)
• Refactored code for collecting and displaying STR variants, which now shares same routines as SV and MEI variants (#5895)
• Deprecate reupload_sv (#5933)
• Dual locus IGV view for BNDs with breaks on different chromosomes (#5939)
• Lazier checking of variant load criteria: most costly query last (#5924)
• Caching variant load criteria queries for considerable speedup for large variant files (#5924)

Fixed

• Fix PanelApp fetch failures caused by 429 responses - Retry-After support (#5864)
• Parsing of REVEL rank score field for LRS from all transcript of a LRS variant (#5860)
• Tests for cli command to update VCF files not running (#5888)
• Gene in panels search results broken layout - overflow when a panel has many panel versions containing the gene (#5899)
• ACMG evaluation PDF export, both style and colors (#5879)
• Genotype query for singletons when not selecting include only in unaffected (#5914)
• Restored Analysis type label on verified/causatives view (#5915)
• Start to end interval search for managed variants (#5917)
• Export causatives from CLI when variant id or quality is unset (#5929)
• Add color to inheritance tags under "Gene annotations", on variant page (#5940)
• STR allele sequences no longer printed in full on general report (#5928)
• gDNA overview in IGV.js undefined loci (#5948)
• ClinGen Criteria Specifications links (CSPEC) on previously submitted ACMG classifications (#5949)

Improved managed variants, deprecation of Python 3.9 & More

[4.106]

Added

• Bulk dismiss STR variants from variantS page (#5774)
• Delete flag for update individual command (#5793)
• Update report command, with a delete flag (#5793)
• Display phase blocks gtf - new key on individuals, parsed from case load config or updated via CLI (#5822)
• Validation of managed variants input (#5842)

Changed

• Refactored variantS pages to share an intermediate template (#5774)
• Removed ClinVar submissions instructions from case pages - it's still present on the ClinVar submissions page (#5806)
• Render the case report's pedigree SVG to a temporary file without Cairo when exporting it to PDF (#5791)
• Deprecate python 3.9 which has reached its EOL, default build to 3.14 (#5818)
• Don't build in editable mode for Docker images (#5819)
• Restored installation of chanjo-report from PyPI (#5820)
• Export of managed variants to VCF is subject to validation. Variants failing validation will raise a warning instead of being included in the VCF file (#5813)
• Reintroduced a link to ClinVar submissions page on variant page - now also for oncogenic variants (#5844)

Fixed

• Filter f hotkey not working on cancer variantS pages (#5788)
• IGV.js updated to v3.5.4 (#5790)
• Broken ClinVar germline submission page when submission contains SVs (#5805)
• Missing size_selector in old filters containing a size criterion, causing the variantS page to crash (#5817 and #5855)
• Avoid backslash in f-strings, to preserve backwards compatibility with old python (#5818)
• GnomAD links for the STR variant page (#5823)
• get_gene_complete_coverage breaking for genes with no intervals on chanjo2, which is returning 'NA' instead of numerical stats (#5830)
• Chromosome order for hg38 in IGV.js view (#5838)
• Clinical filter for outlier variants (#5832)
• Decipher query was treated as a primary - now secondary again (#5832)
• Expansion support display on STR GT card (#5840)
• Keep any active page filters alive when editing/removing managed variants (#5833 & #5836)
• MIM diseases can have multiple descriptions - merge them instead of using the first (#5814)
• Cytobands chrom select undefined at managed variants page load - js console warning cleanup (#5841)
• Cancer case page not showing if a pinned variant is included in an oncogenic ClinVar submission (#5844)
• 429 Client Error: Too Many Requests when updating the PanelApp GREEN panel using the command line (#5849)
• Revert general POST redirect and introduce separate such for managed variants (#5857)
• Prevent false positives in REF/ALT validation of managed variants (#5859)

Downgrade to `igv.js` 3.5.0

[4.105.2]

Fixed

• Downgrade igv.js to 3.5.0 to restore alignment track popupData (#5783)
• CN profile button does not dim for visited links (#5787)

Improved pagination, SV page and paraphase view, added variantS keyboard shortcuts, and much more

Scout version 4.105.1

There was no official 4.105 release, due to an old uv.lock file.

ADMINS - Please note that this release has a (non essential) database index update for the hgnc genes part of the database. If your db is small enough, simply drop indices and rebuild them. Otherwise, run
scout index --update -c hgnc_gene and manually remove the old indices in that collection (all starting with build, leaving only the new build_chromosome_start_end with that prefix).

See PR #5532 for details on updating to chanjo2 with authentication. Essentially, if you enable authentication, also upgrade your chanjo2 service to version 3.9.

We introduce a typo corrected --rank-threshold option alias for the already deprecated one (#5720). If you use this in your workflows, consider if it is a good time to change it. The fallback is scheduled for removal with Scout v5.

For the web user interface, we have introduced some keyboard shortcuts for the variantS pages. Try them out and let us know if they work for you, if you want more or different ones! Excerpt from the updated user guide:

Hotkeys available on all variantS pages

Some variants hotkeys are sensitive to which row you are currently hovering over.

• d for checking Dismiss checkbox on current row
• v for opening a Variant on current row (open the variant, typically in a new _blank tab)

Others give you quick access to a given function.

• c Clinical filter
• f Filter variants
• g focus input on the Gene symbol field, un-collapsing filter if needed
• b toggle dismiss Bar

[4.105.1]

Fixed

• uv lockfile update (#5780)

[4.105]

Added

• Support for variants annotated with an unmodified ClinVar VCF (#5691)
• Parse and display copy number on SV page, genotype table (#5692)
• Bootstrap-based pagination on variantS pages (#5697)
• More transcript insights on variant summary for SV variants hitting max 5 genes (#5706)
• Button to export ACMG classifications to PDF (#5715)
• CLINSIG table on SV variant page (#5718)
• Search genes at breakpoint for larger SVs (#5722)
• Code for refreshing id token, if needed. To be used for authenticated requests to chanjo2 (#5532)
• Genotypes on Search SNVs & SVs page (#5737)
• Display the number of fusion variants on the variantS page, just like the other variant types (#5754)
• Keyboard shortcuts on the variantS pages - see the updated user guide for details (#5768)

Changed

• Better access to ALT allele for SVs (#5694)
• Remove unused variant_count parameter from several functions involved with variant queries (#5700)
• Consolidated and simplified case handling tests (#5708)
• Authorize access to IGV.js track files at endpoint, instead of by session cookie. Allows huge case groups and many open IGV.js sessions. (#5712)
• On the variant page, the corresponding button opens the ACMG and CCV classification tools in a new tab (#5723)
• Fix CLI parameter typo --rank-treshold with backward-compatible alias and deprecation warning (#5720)
• Safer redirect to previous page for all views and controllers still using redirect(request.referrer)(#5721)
• Default paraphase igv.js track settings: color by YC, squish, extend visibility window, auto-height and place last in view. (#5724)
• Chanjo2 requests are sent with OIDC id token, if available (#5532)
• Refactored and simplified SV, cancer SV and MEI variants views (#5701)
• Replaced deprecated flask-ldapconn library with flask-ldap3-login. Modified LDAP login module accordingly (#5719)
• Update IGV.js to v3.5.3 (#5757)
• Specify in the MT report that Chanjo2 stats are based on full chromosomes MT and 14, not transcript intervals. (#5771)

Fixed

• Typo in PR template (#5682)
• Highlight affected individuals/samples on GT call tables (#5683)
• Refactored and simplified the LoqusDB archived observations table. -1 is no longer shown for missing observations (#5680)
• Fix a parsing issue with VEP annotations done with --check_existing where the CSQ key CLIN_SIG would be prioritised over CLINVAR (#5691)
• Display variant rank score 0 (#5699)
• Show only IGV link to breakpoint1 for SVs of sub-category INS (#5694)
• Allow updating case owner on scout load case -u (#5681)
• Missing query results on STR variantS page (#5713)
• Links to variants with missing rank scores from Causatives and Verified pages (#5715)
• Clinical filter button on research variants, wrongly redirecting to respective clinical variants pages (#5725)
• Pagination to handle empty search results (#5727)
• Gene variants page to return all resulting variants again (#5727)
• Gene panel parsing if gene doesn't contain an identifier (#5733)
• Include both chanjo and chanjo2 stats on MT report (#5686)
• Institute cases filtering with Has ClinVar submissions checkbox (#5735)
• Display plain variant rank score also if norm rank score is missing (#5738)
• Missing cairo runtime dependency (#5750)
• Fix pagination for somatic SVs (#5746)
• Fix display of STR MC for cases with GT "./0" calls (#5749)
• Build full HGNC genes for STR variants with HGNCId on load (#5751)
• Use proper end position for large SVs when looking up edge genes (#5755)
• Fixed crash on the Gene Panel page when changes to the same panel version were applied from multiple browser tabs (#5762 and #5765)
• Sort STRs primarily by HGNC symbol, if available (#5763)
• Refresh login token on stale case pages before submitting chanjo2 forms (#5772)
• Safer code in gene panel parsing (#5778)

v4.104 - WUI user edit, more WTS filters, ESCAT cancer SNV tiers, clickable rows

[4.104]

Added

• Parsing variant'slocal_obs_cancer_somatic_panel_old and local_obs_cancer_somatic_panel_old_freqfrom Cancer_Somatic_Panel_Obs and Cancer_Somatic_Panel_Frq INFO keys respectively (#5594)
• Filter cancer variants by archived number of cancer somatic panel observations (#5598)
• Export Managed Variants: CLI now supports --category to filter by one or more categories (snv, sv, cancer_snv, cancer_sv). Defaults to all. (#5608)
• New form to create/edit users on the general users page (visible to admin users only) (#5610 and #5613)
• Scout-Reviewer-Service endpoint to visualise PacBio trgt called expansions (#5611)
• Updated the documentation with instructions on how, as an admin, to add/edit/remove users from the main users page (#5625)
• Button to remove users from the main users page (visible to admins only) (#5612)
• New "P-value, abs log₂FC and abs ΔΨ WTS filters options (#5639)
• ESCAT tiers for cancer SNVs (#5660)

Changed

• Avoid utcnow() deprecated code by installing Flask-Login from its main branch (#5592)
• Compute chanjo2 coverage on exons only when at least case individual has analysis_type=panel (#5601)
• Display conservation scores for PHAST, GERP and phyloP alongside "Conserved" or "NotConserved" (#5593)
• Exporting managed variants from the command line with the --collaborator option will return variants from the specified institute plus those not assigned to any institute (#5607)
• Safer redirect to previous page for variants views (#5599)
• Make whole caseS row clickable link for case page (#5620)
• Make whole variantS row clickable link for variant page (#5618)
• Refined the filtering logic for Clinical WTS variants. The clinical filter now selects variants with either padjust < 0.05 or (p_adjust_gene < 0.1 and abs(delta_psi) > 0.1), for OUTRIDER expression variants and FRASER splicing variants respectively (#5630)
• Removing git installers when building Docker images (#5644)
• Refactored the parsing of the app config file so there exists only one centralized loader for both cli and web app (#5638)
• Restrict gene-overlapping variants (DNA and WTS outliers) search to variants found in affected individuals (#5623, #5659)
• Update command: scout export variants now scout export causatives (backward-compatible) (#5654)
• Show estimated VAF% also for panel and WES SNVs, much as for MT variants (#5658)

Fixed

• Treat -1 values as None values when parsing archived LoqusDB frequencies - works retroactively on variantS page, not on variant page yet (#5591)
• Links to SNVs and SVs from SMN CN page (#5600)
• Consistent panel display on variants pages for unselected "All" panels (#5600)
• Bump tj-actions-branch-names GitHub action to v9 (#5605)
• Missing variant key tool_hits causing fusion variants page to crash (#5614)
• Add/fix conflicts between ClinGen-CGC-VICC classification criteria to fix discrepancies to Horak et al (#5629)
• Fix display of gene symbols for TRGT loci on variantS page (#5634)
• Parse and store also SpliceAI, CADD scores where all scores are 0. (#5637)
• Git missing from docker bookworm slim image (#5642)
• Matching cancer_snv managed variants failure (#5647)
• Parsing of database name when provided on a .yaml config file (#5663)
• Export causatives command crashing on variants that have been removed (#5665)
• Don't follow row link for checkboxes or other input elements (#5668)
• Parse error on REViewer.trgt case load entries (#5672)
• Fix SpliceAI 0.0 score display (#5675)

Full Changelog: v4.103.3...v4.104