Update highlights

[Since 4.59, GMCK-RD theme day 2022-09-28]

ClinVar submission
Phenopacket import and export
Mitochondrial deletion signatures (mitosign) can be uploaded and shown with mtDNA report
List of "safe" gene panels available for matching causatives and managed variants in institute settings, to avoid secondary findings
Remove rerun emails and redirect users to the analysis order portal instead
svdb_origin as a synonym for FOUND_IN to complement set for variants found by all callers [4.58-4.59 Solna 220831-221014]
Additional case category Ignored. Excludes from stats on solved vs archived and doesn't have to be juggled toactive/inactive.
Distinct colors for different inheritance models on RD Variant page
Gene panels PDF export with case variants hits by variant type
Avoid showing case as rerun when first attempt at case upload failed
Filter cases for RNA-seq data (Also prep work for RNA fusion)
Managed variant editing (update from file, without delete)
Refactor for loading custom (html or PDF) reports

Next release (4.63rc) digest

Added

Display data sharing info for ClinVar, Matchmaker Exchange and Beacon in a dedicated column on Cases page
Display dismissed variants comments on general case report
Modify ACMG pathogenicity impact (most commonly PVS1, PS3) based on strength of evidence with lab director's professional judgement
REViewer button on STR variant page
Changed
Display chrY for sex unknown
Fixed
Default IGV tracks (genes, ClinVar, ClinVar CNVs) showing even if user unselects them all
Show matching causatives on somatic structural variant page

News after MIP 11.1

REViewer: Scout-REViewer service integrated. Sync of locus definitions with STipy.
vcf2cytosure
TIDDIT

Information and discussion points

possibility to upload reference and pipeline info for cases. Anyone for having them on all cases, or is asking for them fine for now?
New ClinVar submission form

Open issues digest

For developers with a bit of time to spend on the Scout archipelago:

Chanjo2
Post-pipeline SV matching. Loqusdb / svdb-like overlap clusters native to Scout? Matching causatives, managed variants etc
Regions on gene panels
Selecting PanelApp panels to merge in panels
Semi-automatic ACMG classification

Update from pipelines

nf-core RD
nf-core RNA-fusion
Balsamic

christacosta commented 1 year ago

Hej, for Cancer Scout, if a SV is found as matching causative (on start page), we would like to see the case ID of that other case/other cases (in the variant page). For SNVs we have a list with cases in which the variant has been marked as causative.

dnil commented 1 year ago

Thank you, well spotted! We'll have a look. I'm going to open a separate issue for this so we can track it.

Hej, for Cancer Scout, if a SV is found as matching causative (on start page), we would like to see the case ID of that other case/other cases (in the variant page). For SNVs we have a list with cases in which the variant has been marked as causative.