Visualization (analysis workflow)
As part of this release, igv.js has been integrated into ella as part of a new visualization feature. ella now let's you visualize all variants in an analysis, along with user customizable tracks at three different levels: global (all users), user group and analysis.
ella provides a few special tracks by default:
- Genepanel: Shows the analysis' genepanel.
- Classifications: Shows all classifications present in the database.
- Variants: Shows the analysis variants after filtering.
New visualization feature
Not relevant (analysis workflow)
Variants can now be marked as
Not relevant for the analysis. Such variants can, depending on the user's configuration, be left without a selected class upon finalization of the analysis.
Quick classification (analysis workflow)
A new quick classification view is now available, aimed at certain workflows for large analyses with many variants.
It gives a summary of the most important information necessary for classifying variants as
Not relevant or
It is most relevant for workflows where you first perform a quicker interpretation of certain variants, before doing a more thorough interpretation of the remaining ones.
Quick classification view
QUALITY card renamed to ANALYSIS SPECIFIC (analysis workflow)
The card in
Classification view previously referred to as
QUALITY is now called
ANALYSIS SPECIFIC to highlight the fact that it's not part of a variant's classification, but rather just a part of the analysis.
The card is blue and collapsed by default, to further separate it from the classification related cards.
Improved view of existing and current class in sidebar (analysis workflow)
The view of a variant's class in the sidebar has been improved.
Left number is existing class, right is new. An arrow indicates that a new classification will be created. Blue background indicates that the variant has been reviewed. You can toggle the review status by clicking on the class in the sidebar.
New user manual
A new, online user manual is now available from within ella itelf. You can access it by clicking
Documentation in the top navigation bar in the overview.
- Visualization (analysis workflow)
- Ability to mark variants
Not relevant(analysis workflow)
- Quick classification (analysis workflow)
- Filters and their parameters are now configurable per user group
- New filter: Quality
- Region filter now can save variants with certain (configurable) consequences from being filtered.
- New variant warning: HGVSc and HGVSp mismatch between corresponding Refseq and Ensembl transcripts.
- Integrated documentation within ella
Other additions and fixes
- Filtered variants are now shown as a list (analysis workflow)
QUALITYcard is renamed to
ANALYSIS SPECIFIC(analysis workflow)
- Improved view of class in sidebar (analysis workflow)
- Workflows can now be finalized with technical, not relevant and/or missing classifictions (depending on configuration). Workflows can still force valid classifications for all variants if desired (old behaviour). (analysis workflow)
Requested dateis now read from input
.analysisfile and used in overview.
- Too wide images in comments will not make the page scrollable in the horizontal direction.
- Overview comment is now visible for
Finalisedanalyses and variants in overview.
- Low quality warning is removed for Sanger variants, as there is no quality data.
- HTML content is now properly sanitized when pasted into comment fields.
- Fix issue where technical status was not reflected in the
TECHNICALbutton in the
QUALITYcard under certain conditions.
- Fix issue where image could not be resized in reference evaluation.
ella now lets you interpret analyses with variants that have been joint called within a single familiy.
The following segregation models are supported:
- De novo
- Autosomal recessive homozygous
- X-linked recessive
- Compound heterozygous
The most powerful filtering requires two parents to be present in the analysis, but some segregation filters and tags also apply to analyses with only siblings (unaffected and/or affected).
Segregation tags in sidebar
Variants filtered out by these filters can be found in the
Segregation category in the excluded variants.
The analysis and variant workflows now have their own
Work log. The work log currently lets you:
- Update the
- Clear any analysis warnings (analysis only). Clearing a warning makes the warning tag disappear from the Overview.
- Adjust the priority of the analysis or variant
- Add messages that should be available to yourself or later interpreters about things that are relevant for the interpretation of the analysis or variant. Messages can contain formatting and images, and are editable until the next interpretation round is started.
All options in the work log can be changed at any time, without having to start a new interpretation round.
Work log example
If there are any messages since last time the workflow was
Finalised, the work log button will appear in purple, along with the current message count.
2 messages since beginning or last finalisation.
Variants are now tagged with warnings whenever there is something special that considered for the variant in question. The list of warnings will be expanded later, but currently includes:
- Worse consequences in other transcripts
- Other variants are within 3 bp of the variant in the analysis
Variant warnings are implemented for both the variant and analysis workflows, but some warnings are only available for analyses.
Warning tags in sidebar.
- Support for family data
- Segregation filter and tags
- Work log
- Variant warnings
Other additions and fixes
Qualityis now it's own section in Classification view (analysis only)
- Quality verification for variants in an analysis (
Technical) is moved from the Info view to the Quality section in the Classification view.
- Variants marked as
Technicalare moved to it's own list in the sidebar.
- Improvements in display of variants with multiple selected transcripts.
Additions and fixes
- Add red 'HOM' tag to top variant bar in order to improve homozygous visibility.
intronfilters into a new, improved
- Improve search performance (entering a gene is now required for searches using HGVS nomenclature).
- Show more information about the available samples in import view
- Add new external database for gene TP53
- Fix missing Hemi total count for gnomAD
Additions and fixes
- Add BRCA Exchange to external databases for BRCA1 and BRCA2
- Add ability to search using genomic position on format g.123456
- Keep existing reference evaluation data when clicking 'Ignore'
- Fix link and reference description in reference evaluation window.
- Fix issue where some variants would appear with two genepanels in variants overview
- Fix issue where worst consequence would not display correctly for a rare case with variant having intron_variant as consequence in one transcript and splice_region_variant, intron_variant as consequences in another transcript.
- Fix issue importing Pubmed XML data for some references.
New import functionality
Requires access to the import view.
ella now lets you re-import previously run samples, using either an existing genepanel or a genepanel customised for that specific sample.
This lets you request new analyses directly in the application and shortens the time for reanalysis with a different set of genes.
Frontend code improvements
The frontend code has been refactored to make it more responsive and to make it easier to add new functionality going forward.
Other additions and fixes
- Display number of excluded references on 'SHOW EXCLUDED' button
- Remove scrollbar on comment fields.
- When there are multiple transcripts in a genepanel, sort them by name. Also display all transcripts in more places, for example in the variants overview.
- Do not add references with Relevance: 'No' to the excluded references list.
- The 'ADD EXCLUDED' window for adding excluded variants now loads faster.
- Search results will now show correctly when typing quickly.
- Many other smaller UI fixes