V33 Patches

Patches	Date
V33.3	June 19th, 2024
V33.2	Feb 18th, 2024
V33.1	Jan 14th, 2024

V33.3 hotfix released for the following issues:

• Analysis Tools | Preset filters | Fixed an issue introduced with v33.2 that caused some LOF preset filters to not return variants. Customers impacted by this issue were notified individually and resolution offered for potentially affected cases.

• Propagation of fixes included in v32.4. See release notes for detail.

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V33.2 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 | 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 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.

• Variant Page | Fixed incorrect gnomAD link after the gnomAD v4 release.

• 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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V33.1 hotfix released for the following issues:

• Add New Case | Fixed issue where new ethnicities added in v32 were not supported for reanalysis in subsequent versions.

• Batch Upload | Fixed issue for singleton cases uploaded with batch uploader that resulted in inability to edit cases after creation.

• Batch Upload | Fixed issue causing Not Authenticated error for customers with more than 100 BSSH projects.

• Batch Upload | Improved backward compatibility for Gender changed to Sex field.

• Pipeline | Improved error logging for DRAGEN for easier troubleshooting.

• Pipeline | Fixed issue where ingesting DRAGEN ExpansionHunter and SV caller VCFs from DRAGEN 4.2 failed cases due to unexpected header.

• Pipeline | SMN Caller | Fixed multiple issues causing case failures from FASTQ & BAM.

• Pipeline | SMN Caller | Fixed issue for GRCh37 & SMN caller where relatedness isn’t calculated due to Peddy failure.

• Pipeline | Enable flow where in a trio only the Proband has Ploidy outputs and parents don’t.

• Pipeline | Don’t fail cases where no samples are provided but ignore samples isn’t set.

• AI | Include full gene list in Phenomeld for virtual panels, irrespective of phenotypic match.

• Cases Page | Search from the cases page is now limited to case ID, sample name and test data fields to improve performance.

• Lab Page | Fixed issue of no coverage statistics for cases with missing samples. Coverage appropriately generated for the samples submitted with the case.

• Lab Page | Fixed missing average coverage affecting some pipelines.

• Analysis Tools | Manually Added Variants | Fixed an issue where STR manually added variants can’t be tagged or reported.

• Analysis Tools | Export | Resolved issue in export of some presets and filters due to incomplete customer facing role.

• Variant Page | Fixed issue where proband coverage copied to parents for customers starting from joint gVCF.

• Variant Page | Fixed all broken gnomAD links after the gnomAD v4 release.

• Variant Page | Updated Decipher link after link structure change.

• Curate | Fixed issue where selecting a disease associated with a gene for a variant appears to automatically apply it to all variants in that gene in the UI, while data is correctly applied in the backend.

• Curate | Enable customers to login to Curate when signed into a different organization on Analyze.

• Reanalysis | Fixed backward compatibility issue preventing variants in cases originally analyzed on and before V27.0 to be pushed into a report.

• Settings | Fixed issue where S3 credentials couldn’t be generated for long domain names. Character limit is eliminated.

• Settings | Fixed issue in kit BED validation for non-canonical chromosomes.

• Infrastructure: Multiple improvements of resource allocations to increase robustness and performance.