IGV 2.0 and bugfixes

Added

• Description of Scout branching model in CONTRIBUTING doc
• Causatives in alphabetical order, display ACMG classification and filter by gene.
• Added 'external' to the list of analysis type options
• Adds functionality to display "Tissue type". Passed via load config.
• Update to IGV 2.

Fixed

• Fixed alignment visualization and vcf2cytosure availability for demo case samples
• Fixed 3 bugs affecting SV pages visualization
• Reintroduced the --version cli option
• Fixed variants query by panel (hpo panel + gene panel).
• Downloaded MT report contains excel files with individuals' display name
• Refactored code in parsing of config files.

Safer CLI and update requirements to use PyYaml >= 5.1

• update requirement to use PyYaml version >= 5.1
• Safer code when loading config params in cli base

CLI running in the app_context and phenotype (HPO) similarity algorithm

[4.5.0]

Added

• Search for similar cases from scout view CLI
• Scout cli is now invoked from the app object and works under the app context

Fixed delivery report upload via API

[4.4.1]

Added

• Display SV rank model version when available

Fixed

• Fixed upload of delivery report via API

MatchMaker Exchange integration

[4.4.0]

Added

• Displaying more info on the Causatives page and hiding those not causative at the case level
• Add a comment text field to Sanger order request form, allowing a message to be included in the email
• MatchMaker Exchange integration
• List cases with empty synopsis, missing HPO terms and phenotype groups.
• Search for cases with open research list, or a given case status (active, inactive, archived)

Fixed

• Variant query builder split into several functions
• Fixed delivery report load bug

Different individual table for cancer cases and bugfix

[4.3.3]

Added

• Different individual table for cancer cases

Fixed

• Dashboard collects validated variants from verification events instead of using 'sanger' field
• Cases shared with collaborators are visible again in cases page
• Force users to select a real institute to share cases with (actionbar select fix)

ClinSig filter fix, search all variants across cases and improved variant reports

[4.3.2]

Added

• Dashboard data can be filtered using filters available in cases page
• Causatives for each institute are displayed on a dedicated page
• SNVs and and SVs are searchable across cases by gene and rank score
• A more complete report with validated variants is downloadable from dashboard

Fixed

• Clinsig filter is fixed so clinsig numerical values are returned
• Split multi clinsig string values in different elements of clinsig array
• Regex to search in multi clinsig string values or multi revstat string values
• Upload VCF files with no variants now works
• Combined Pileup and IGV alignments for SVs having variant start and stop on the same chromosome

Validated export

Added

• Show calls from all callers even if call is not available
• Instructions to install cairo and pango libs from WeasyPrint page
• Display cases with number of variants from CLI
• Only display cases with number of variants above certain treshold. (Also CLI)
• Export of verified variants by CLI or from the dashboard

Fixed

• Fixed code to extract variant conservation (gerp, phyloP, phastCons)
• Visualization of PDF-exported gene panels
• Reintroduced the exon/intron number in variant verification email
• Sex and affected status is correctly displayed on general report
• Force number validation in SV filter by size
• Display ensembl transcripts when no refseq exists

MT export

Added

• Mosaicism tag on variants
• Show and filter on SweGen frequency for SVs
• Show annotations for STR variants
• Show all transcripts in verification email
• Added mitochondrial export
• Adds alternative to search for SVs shorter that the given length
• Look for 'bcftools' in the set field of VCFs
• Display digenic inheritance from OMIM
• Displays what refseq transcript that is primary in hgnc

Fixed

• Archived panels displays the correct date (not retroactive change)
• Fixed problem with waiting times in gene panel exports
• Clinvar fiter not working with human readable clinsig values

Fixed panel upload

Fixed

• Fixed gene panel create/modify from CSV file utf-8 decoding error
• Updating genes in gene panels now supports edit comments and entry version