V34 Patches
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Last updated
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| Patches | Date |
|---|---|
V34.7 | August 13, 2024 |
V34.6 | August 6, 2024 |
V34.5 | June 19, 2024 |
V34.4 | May 17, 2024 |
V34.3 | May 5, 2024 |
V34.2 | April 18, 2024 |
V34.1 | Feb 21, 2024 |
This hotfix enables an update of gnomAD 4.1 non-UK Biobank data for SNV.
Due to the extensive changes required to update from gnomAD 4.0 to gnomAD 4.1 non-UKB data, the new gnomAD data will be turned off by default, as we believe some re-verification may be needed before switching to gnomAD 4.1 non-UKB.
A parameter in organization settings, configurable by Illumina support teams has been added to define the gnomAD version.
The default configuration is for gnomAD_version 4.0.
Illumina support teams can update this to gnomAD_version 4.1_non-UKB.
This parameter can be configured independently in staging and production environments for customers on Professional or Enterprise plans.
The population summary tab will clearly note whether gnomAD or gnomAD non-UKB was used.
When updating to the gnomAD 4.1 non-UKB data, links will be directed to the non-UKB data.
Versions tab will display the specific gnomAD version used.
This organization setting will be deprecated in the release of V36.0.0, at which time gnomAD 4.1 non-UKB will be the default gnomAD annotation within the Emedgene software.
Variant Page | Fixed an issue where in some cases OMIM inheritance modes were incorrectly displaying CGD values.
The following fixes are aimed at improving application performance for customers using older personal computers with lower available RAM.
General | Software will display a performance warning when less than 2Gb of free RAM is available.
Visualization | Using a desktop IGV version and disabling the embedded IGV will reduce the memory requirements for the Emedgene application.
Disable embedded IGV by toggling embedded IGV off and desktop IGV on in the side car links.
Push all tracks to desktop IGV. When loading tracks to desktop IGV, now all available tracks will be automatically pushed, with the exception of the ClinVar SV known variant track.
Variant Page | Embedded IGV | Improved IGV performance by reducing API calls when moving between variants.
Additional fixed issues:
Add New Case | When running a case for a kit that previously had an associated PON, case will fail if PON isn’t attached to the kit. This will help mitigate case runs where the DRAGEN version is updated but no new PON is created.
Edit Case | Fixed a bug resulting in long reanalysis times when only phenotypes were updated in a case.
Lab Tab | Lab Tab | Fixed a bug resulting in no data loaded to the lab tab for new organizations.
Analysis Tools | Filters | Fixed a bug for Variant Effect Filters, when moving from simple to advanced, not all variant effects were available for filtering, which also caused a variant count discrepancy.
Analysis Tools | Preset Filters | Fixed a bug that always showed the description of removing polymorphic variants as ‘Display polymorphism: True’ although the behavior of the filter correctly removed the variants.
Variant Page | Related Cases | Fixed an issue intermittently causing related cases component to fail to load when moving quickly between variants.
Export | Fixed a bug failing the export of parental data for some customers.
Curate | Gene search now excludes variant interpretation paragraphs in order to prioritize gene entity retrieval.
Settings | Illumina clouds only, ‘See more’ button fixed, it was disabled by v34.4.
Add New Case | For customers pushing the SNV VCF for DRAGEN 4.2 and 4.0, variants with the targeted tag will be skipped as they cause the pipeline to fail.
Edit Case | Fixed an issue that failed an edit for cases starting from FASTQ, when new family members were added. The flow of adding family members to an existing case is a supported flow.
Lab Tab | Fixed an issue where when selecting other family members UI indication of selected sample was unclear due to missing borders on the selection.
Lab Tab | Fixed an issue that caused average quality percentage to be above 100%.
Analysis Tools | Presets Schema V2 | Added the possibility to create strictly greater filters on the MQM field to the preset schema.
Analysis Tools | Filters | Added gnomAD 4.0 GRCh38 MID EAST population to the af_max_any_pop calculation.
Variant Page | Added the gnomAD 4.0 Mid East exome data to Population Statistics.
Variant Page | Fixed an issue where when a variant was tagged there was a delay before the auto generated interpretation text was loaded, during which customers may have started to write an interpretation and it was deleted.
Variant Page | Visualization | Fixed an issue which rarely resulted in an ‘MD5 checksum issue’ error message on the embedded IGV.
Curate | Gene search now excludes variant interpretation paragraphs in order to prioritize gene entity retrieval.
Settings | Illumina clouds only, ‘See more’ button fixed, it was disabled by v34.4.
Hotfix released for the following issue:
Illumina Clouds | Fixed an issue where some users on Illumina clouds could not log into Emedgene. All users must now login using their direct organization URL for their private domain in the Illumina cloud.
Hotfix released for the following issues:
Add New Case | Fixed batch case creation issues to re-allow empty sample names and enable upload of validated file.
Candidate Page | Fixed display of gene in a CNV to match evidence graph gene. Previous fix only covered compound heterozygous variants.
Variant Interpretation Template | Fixed issue preventing enrichment of template with ACMG classification on V34.
Export | Fixed an issue preventing export of data from analysis tools if column exceeds csv file limitations. Data will be truncated with a comment.
Organization Settings | Webhooks | Fixed another issue preventing the trigger of webhooks on cases that transitioned automatically to the ‘Delivered’ status on ILMN clouds.
Organization Settings | Webhooks | Improved webhook robustness by making webhook statuses case-insensitive, can be capitalized or not.
Hotfix released for the following issues:
General | Users on Illumina clouds will now get a warning when they are logged out due to their IAM settings. The warning will prompt for a refresh, preventing loss of work on the Emedgene software.
Pipeline | Pipeline will no longer fail cases with empty VCFs.
Candidate Page | Fixed issue where displayed gene on candidate page differed from gene in evidence graph/analysis tools.
Lab Tab | Updated case quality tooltips for increased clarity and accuracy.
Analysis Tools | Fixed issue where empty evidence graph for Manually Added Variants and large SVs prevented editing of evidence and also caused activity loop.
Analysis Tools | Fixed issue where multi-select caused extra spacing in table rows.
Variant Page | Visualization | Improved performance of visualization component.
Variant Page | Fixed issue where gnomAD mtDNA total AF, homoplasmy count, heteroplasmy count and max AF were erroneously displayed as 0 on the variant page. Preset filters were unaffected by this issue.
Variant Page | Fixed an issue where MitoTip prediction score quartiles were mislabeled, although the score appears correctly.
Variant Page to Curate | Fixed an issue where variants curated after initial case run appeared with ‘Export to Curate’ button, instead of ‘Open Curate’.
Variant Page | Updated Orphanet links to new Orphanet structure.
Report/Export | Reporting/exporting insufficient coverage regions will now require an organization setting, explicitly selecting only one coverage threshold - 0X, 5X, 10X, 20X, or ALL. This will resolve any issues with reporting insufficient coverage regions.
Dashboard | Activity Sidebar | Fixed an issue where clicking on a case ID from the activity sidebar did not work.
Organization Settings | Presets V2 | Improvements to backward compatibility with Presets V1 to enable seamless customer migrations to new tool.
Special characters [&, %] allowed in preset name
emg_qual_allele_bias and constraint_mis now accept integer or decimal numbers.
Any field that accepts a decimal number can now accept a value of 0.
Pathogenicity exclusions now includes ClinVar ‘starred_statuses’: ‘criteria provided, conflicting classifications.
Organization Settings | Webhooks | Fixed an issue where webhooks were not working for the cases ‘Delivered’ status on ILMN clouds.
Hotfix released for the following issues:
Add New Case | NovaseqX added to selectable sequencers.
Add New Case | Fixed a batch uploader issue where sex column was used correctly but also imported in additional data.
Pipeline | Fixed an issue where cases running with DRAGEN 4.2 on HG19 fail the pipeline.
Pipeline | In alignment with DRAGEN recommendations for the SV caller, when variants are larger than 50Kb they will automatically be marked as low quality in order to reduce the number of artifacts shortlisted by the AI and highlighted for review. This affects all DRAGEN versions once a pipeline is updated to v34.
Pipeline | Added support for multi-allelic CNVs when customers start from joint gVCF.
Pipeline | Added support for DRAGEN VCFs where hardware is unknown.
Pipeline | Fixed a bug that caused discordant AI results between a first and second analysis due to model selection.
Pipeline | Fixed an issue causing some reanalysis cases to fail due to insufficient backward compatibility with previous values. This fix will improve pipeline robustness.
Cases Page | A search on this page will only search for EMG ID, sample names, or any string in the test data. This fix will improve performance.
Analysis Tools | Fixed intermittent issue causing no variants to load in the variant grid for certain screen sizes and number of variants.
Analysis Tools | Fixed erroneously generated duplicate and additional columns (e.g. mother_zygosity).
Analysis Tools | Fixed variant count issue for compound heterozygous filters caused by using a single source for what is essentially a two-step process. Only count displayed was incorrect.
Analysis Tools | Fixed preset filter issue where presets were returning more results than expected due to ‘-‘ in the gene name in some preset filters. No data was missed.
Analysis Tools | Fixed issue where ‘greater than’ preset filters also returned a 0 value.
Analysis Tools | Fixed an issue where after hitting the clear all filters you can no longer save a new preset (refresh was the workaround).
Analysis Tools | Presets and Preset Groups will include support for some special characters that are in use in legacy presets (e.g. < >).
Analysis Tools | Preset filters | Clear save error message after correcting the name.
Analysis Tools | Fixed an issue where variant tagging or pathogenicity changes are not disabled after case is finalized, when multi-select is enabled.
Organization Settings | Fixed an issue causing available URLs to become unviewable when changing the platform version from V34 to V33.
Performance: Additional updates to increase performance through infrastructure modifications.
