Scout user meeting agenda 17/2 -21

henrikstranneheim commented 3 years ago

Welcome to the Scout user meeting @9:00-10:30 am!

However, due to the current situation we will aim to host this on zoom.

Location: https://ki-se.zoom.us/j/68072958794

Please help us fill the agenda with topics that may interest you.

Agenda

Issue discussion points

Remove length filter from clinical sv filter
Suggestion: remove OMIM panel (from comments)
Suggestion: direct link to IGV from case page

New features & changes since last meeting

[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 (dbVar Pathogenic or Likely Pathogenic hosted on figshare)
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 (custom igv tracks hosted on figshare)
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 (not yet in production)
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 (who's using this feature, can we remove it?)
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 (link)
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

[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 (fixed on igv.js 2.7.5 released today)
Revert CORS-anywhere and introduce a local http proxy for cloud tracks

[x.x]

Added

Introduced a reset dismiss variant verb
Button to reset all dismissed variants for a case
Add black border to ideograms
Show ClinVar annotations on variantS page
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
Changed
Cancer variants table header (pop freq etc)
Only admin users can modify LoqusDB instance in Institute settings
Switched to igv.js 2.7.5
Style of case synopsis and variants and case comments

CG (Solna)

synopsis, cohort, phenotype_terms
Chromograph (re)enabled

On the horizon

better loqusdb integration
new major version brewing
MIP-RD RNA integration
db server move (Solna) timeline

lcovill commented 3 years ago

Part question part suggestion: is there a way to remove/tailor HGNC symbol search history? Would be great to be able to de-clutter.

northwestwitch commented 3 years ago

Part question part suggestion: is there a way to remove/tailor HGNC symbol search history? Would be great to be able to de-clutter.

Hi @lcovill browser search history doesn't depend on the settings on our side. Scout is like all the other websites and search history is something that is specified on your browser setup (client-side). Check out this post that explains how to set up autofill data on different web browsers. Cheers, Chiara

northwestwitch commented 3 years ago

Suggestion: remove OMIM genes panel

Clinical-Genomics / scout