# Release notes: Latest releases

Major versions Minor versions
v1.16 v1.16.1, v1.16.2
v1.15 v1.15.1
v1.14 v1.14.1, v1.14.2
v1.13 v1.13.1, v1.13.2

See older releases for earlier versions.

# Version 1.16.2

Release date: 21.12.2021

# Highlights

This is a bugfix release.

# All changes

  • Fixed a bug where genotype display is not shown in allele bar

# Version 1.16.1

Release date: 16.12.2021

# Highlights

This is a bugfix release.

# All changes

  • Fixed a bug causing inability to paste plain text into comment fields.
  • Fixed word wrapping in comment fields.

# Version 1.16

Release date: 16.12.2021

# Highlights

# Experimental support for CNV interpretation

This version introduces experimental support for copy number variants (CNVs).

When enabled, a separate CNV mode is added (switched to using a button in the top bar), where CNVs are shown in a separate variant list and allow documenting, reporting and reusing CNV interpretations, as for SNVs. The current version supports CNV deletions, duplications and tandem duplications (VCF format: DEL, DUP and DUP:TANDEM, respectively; for variants of type = SVTYPE).


Figure: Experimental CNV mode. Major changes from SNV mode are highlighted with red squares.

Note the limitations in this version:

  • No CNV filtering is done in ELLA, for the time being this needs to be done upstream, prior to import.
  • No particular adaptations have been made to presentation of annotation. However, any annotation from the VCF can be added in the configuration, and we recommend adding CNV-specific tracks to VISUAL to aid in interpretation.
  • No CNV-specific ACMG criteria have been added.
  • No manual import of CNVs is supported.

DISCLAIMER

As the CNV features are not fully validated, this functionality is currently disabled by default, and we recommend not enabling it in production. For testing, the new features can be enabled by setting the feature flag ENABLE_CNV to true in the application configuration.

# Changes in VISUAL

Configuration of tracks in VISUAL has been further improved, allowing all types of tracks to be placed under presets. To allow better zoom/scroll control with many tracks visible, this version also adds a requirement to hold the Shift or Alt key when zooming with the mousewheel.

# πŸ”Ί Breaking changes

# Configuration of tracks in IGV

With this version, configuration of tracks shown in IGV needs to be updated.

Specifically, all tracks are now configured in a single config file and specified as either DYNAMIC, STATIC or ANALYSIS tracks. This means all tracks (including dynamic and analysis tracks) are now configurable, but also means that the individual track JSON config files used in earlier versions will no longer work.

To configure a particular track, the file path must be matched with a regular expression (regex). Note that the JSON format requires special regex characters to be double-escaped (e.g. .bed.gz should be written as \\.bed\\.gz). See /src/vardb/testdata/igv-data/track_config_default.json for examples and IGV in VISUAL for further details.

# All changes

# Version 1.15.1

Release date: 10.11.2021

# Highlights

This is a bugfix release.

# All changes

  • Fixed a bug causing missing transcripts in exported classifications.
  • Fixed a bug causing an error when listing "5 most similar gene panels" for analyses with custom gene panels.
  • Fixed a bug causing IGV search to occasionally return wrong gene when there are partial matches.
  • Fixed a bug causing invisible INH values for filtered variants.
  • Upgraded IGV.js in VISUAL to v2.10.4 (opens new window).
  • Fixed a bug causing error on start if a Worklog comment was just added.

# 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.

# πŸ”Ί 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 β‰₯0.7 (was β‰₯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).

# πŸ”Ί 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

Last Updated: 12/21/2021, 8:58:33 AM