# Release notes: Latest releases

Major versions Minor versions
v1.14 v1.14.1, v1.14.2
v1.13 v1.13.1, v1.13.2
v1.12 v1.12.1, v1.12.2, v1.12.3

See older releases for earlier versions.

# Version 1.15

Release date: 13.10.2021

# Highlights

This update brings a number of enhancements to the user interface, with further improvements to VISUAL, new quick add actions, as well as several smaller improvements and bugfixes.

# Improvements to VISUAL

Selecting tracks in VISUAL has been further improved by splitting off presets in one section and the individual tracks in another, with the latter section collapsed by default. Tracks are now also organized under headers determined by preset names instead of the previous "Global", "Group" and "Analysis" headers:

Figure: Improved track selection presets, with tracks organized by preset name.

Note that tracks that have no configuration (e.g. at present, analysis raw data) are placed in the preset OTHER .

In addition, IGV.js was upgraded to the most recent version (opens new window), which adds exon numbering (in feature popup) to transcript reference tracks, and improved performance. It is now also possible to open analyses with no unfiltered variants, e.g. for reviewing raw data before reporting negative test results.

See Visual for further details.

# New quick add actions

It is now possible to quickly add a signature and date ([username, yyyy-mm-dd]) to any comment field, using either the keyboard shortcut Alt + S or a button on the formatting toolbar:

Figure: Quick add signature to any comment field.

In addition, the option to quickly add a reference was added to the Report and Indications comment fields on the REPORT page, as well as in the Indications comment in the sidebar:

Figure: Quick add references to Indications or Report comments.

Note that for these particular comment fields, only references from variants that have been included in the REPORT are listed.

# Miscellaneous improvements to the user interface

Other user interface changes in this version include a better collapsed mode for sections on the CLASSIFICATION page, more concise gene and gene panel related information, improvements to layout, and various bugfixes.

# All changes

# Version 1.14.2

Release date: 31.08.2021

# Highlights

This release adds a few bugfixes.

# All changes

  • Fixed a bug causing inability to import VCFs with no variants.
  • Fixed missing tooltip for reference title.
  • Fixed a bug causing incorrect sorting of variants in the Region section.
  • Fixed a bug causing display of info from currently selected variant instead of filtered variant in Filtered variants modal.
  • Fixed a bug causing inability to manually add External or Prediction info in certain instances.
  • Fixed a bug causing missing hemizygous counts for legacy/default frequency annotation.

# Version 1.14.1

Release date: 08.07.2021

# Highlights

This release adds a single bugfix.

# All changes

  • Fixed a bug causing front end to break in some edge cases.

# Version 1.14

Release date: 30.06.2021

# Highlights

The most significant change in this release is the addition of support for configurable annotation. In addition, several improvements have been made in the UI in preparation for CNV support.

# Support for configurable annotation

Adding new kinds of variant annotation in ELLA has up until now required changes to the source code, and has been a major limitation in the software. Starting with this release, however, new annotation can be added with a few changes to configuration. This allows much more flexibility and ease when adding new variant annotation resources. See the technical docs for more information on how to use the new configuration.

Unless new annotation is added, no changes will be visible to the end user, except a very minor change in the sorting of ClinVar entries (now sorted on date only).

# New REGION section

A new section termed REGION has been added to the CLASSIFICATION page. This shows previously classified SNVs from the internal database VarDB that are within a preconfigured genomic distance from the currently selected variant:

Figure: New section with nearby classified variants.

# Improvements to VISUAL

This version adds several improvements to how the VISUAL mode (with IGV.js) works. Most significantly, the track selection section on top of the VISUAL page is now collapsible and has the possibility for adding presets that allow quick selection/deselection of groups of tracks:

Figure: Improved track selection with possibility for presets.

In addition, the Classification track now includes links to existing allele assessments. Click a variant in the track, then the link in the resulting popover to go to the variant:

Figure: Classification track now has links to existing allele assessments.

Lastly, it is now possible to zoom the view quickly using the mouse wheel, and clicking a selected variant in the side bar recenters the view on the variant.

# 🔺 Breaking changes

The following changes must be made to ella-config.yml to use this version:

  • Remove frequencies.view and instead add to the new annotation-config.yml (see Annotation).
  • Add similar_alleles with subkeys max_variants and max_genomic_distance (see Region).

# All changes

# Version 1.13.2

Release date: 19.05.2021

# Highlights

This release changes thresholds for verification warnings and adds a few other tweaks and bugfixes.

# All changes

  • Thresholds for the "Needs verification" warning was adjusted to depth <20 (was ≤20) and allele ratio (heterozygous) ≤0.3 or ≥0.7 (was ≥0.6).
  • Disallow spaces and underscores in custom gene panel names when ordering reanalyses in the IMPORT module.
  • Fixed a bug causing de novo likelihood calculation to fail in certain instances.
  • Fixed a bug causing missing source information for studies and references.

# Version 1.13.1

Release date: 16.04.2021

# Highlights

This release adds a single bugfix.

# All changes

  • Fixed a bug causing excessive load on backend.

# Version 1.13

Release date: 09.04.2021

# Highlights

This release brings several improvements to variant filtering rules, as well as a number of smaller fixes.

# Improvements to variant filters in ELLA

It is now possible to configure the Classification filter to only consider classifications that are still valid. With this option enabled it is possible to define that e.g. class 1 and class 2 variants should be filtered only if they have a classification that is still valid (not outdated).

# Improvements to pre-filters

The pre-filters (applied before import of variants into ELLA) are now configurable and has the added option of pre-filtering variants with low mapping quality (MQ<20). This latter option is relevant e.g. for variants called with Dragen-GATK, which unlike GATK does not automatically exclude variants with a low MQ.

# Upgraded IGV in VISUAL

IGV.js on the VISUAL page has been upgraded to v2.7.9 (opens new window). For ELLA users, this fixes a few bugs, but also brings new view mode options: Click the cog wheel to the right of a track to switch between "expand" (default), "squish" or "collapse" display modes (available options depend on track type).

# 🔺 Breaking changes

With the improvements to pre-filters, the configuration in usergroups.json must be updated. The equivalent to the previous "prefilter" = True is now "prefilter": [["hi_frequency", "no_nearby_variant", "no_classification", "not_multiallelic"]]. See pre-filters for further details.

# All changes

# Version 1.12.3

Release date: 19.02.2021

# Highlights

This release adds a few bugfixes.

# All changes

  • Fixed a bug causing loading of certain historical analyses to fail.
  • Fixes to deposit and backend.

# Version 1.12.2

Release date: 29.01.2021

# Highlights

This release adds a few bugfixes.

# All changes

  • Fixed a bug causing ELLA not to start.
  • Fixed a bug causing excessive memory use in exports of variant interpretation database.
  • Fixed an error in test configuration.

# Version 1.12.1

Release date: 19.01.2021

# Highlights

This release adds a few bugfixes.

# All changes

  • Fixed a bug that caused pre- and postprocessing to fail.
  • Fixed a bug that caused missing "Requested" date on imported analyses.
  • Fixed a bug that caused performance problems.

# Version 1.12

Release date: 13.01.2021

# Highlights

This release includes many fixes and improvements, both to the frontend and backend/development environment. The most significant changes for users include changes to classification, history and variant warnings:

# Redefined classification choices

Variant classification choices have been redefined in line with ClinVar definitions (opens new window):

  • CLASS U was renamed to NOT PROVIDED, meant for recording various information (literature/research/clinical/phenotyping) without interpreting clinical significance. It is recommended to configure this class to be immediately outdated.
  • The choice RISK FACTOR was added, meant for variants that are interpreted not to cause a disorder but to increase the risk.

The classification choices are now:

Figure: Redefined variant classification choices.

# Improvements to history

History for changes to the variant CLASSIFICATION REPORT field was added, and the HISTORY pop-up now shows a drop-down for viewing previous versions instead of listing them:

Figure: Modified variant history view with addition of Report history and drop-down for previous versions.

In addition, when opening a previously finalized analysis, ELLA will now default to displaying the state corresponding to the latest interpretation round, i.e. showing variant interpretations, classifications and annotation exactly as they were presented at the time of the last finalization. The previous default, CURRENT DATA (along with any other interpretation round), is still available using the drop-down in the top bar. To prevent confusion, a warning was added when viewing historical data.

Figure: Latest interpretation round now selected by default (with warning) for historic analyses.

# Improved warnings

To improve visibility of the different variant warnings displayed on the CLASSIFICATION page, collision warnings are now shown in a yellow banner separate from annotation and user group warnings (red), and collision warnings are no longer included in the ! tag in the sidebar:

Figure: Collision and annotation warnings are now separate.

In addition, ELLA now displays a message at the bottom of the page if a finalized variant in an ongoing analysis has been updated and finalized by another user:

Figure: Message when evaluation has been updated by another user.

Note that the message is only displayed when a user finalizes another variant or manually refreshes the view.

# Select user group on custom imports

To better support custom gene panel imports that should be available to more than one user group, the custom gene panel import dialogue now includes an option to select user groups:

Figure: Message when evaluation has been updated by another user.

# All changes

Last Updated: 10/11/2021, 9:17:07 AM