V34 Patches
| Patches | Date |
|---|---|
V34.5 | June 19th, 2024 |
V34.4 | May 17, 2024 |
V34.3 | May 5, 2024 |
V34.2 | April 18, 2024 |
V34.1 | Feb 21, 2024 |
V34.5 Update (June 18th, 2024)
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.
V34.4 Update (May 17th, 2024)
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.
V34.3 Updates (May 5th, 2024)
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.
V34.2 Updates (April 18th, 2024)
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.
V34.1 Updates (February 21st, 2024)
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.
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