Emedgene
Illumina Connected Software
  • Get Started with Emedgene
    • Get started with Emedgene
    • How can Emedgene help you solve a case?
  • Emedgene analyze manual
    • Getting around the platform
      • Top navigation panel
      • Emedgene Applications menu
      • Dashboard
      • Settings
      • User roles
      • Help
      • Okta identity management
    • Managing data storage
      • Manage data storages
      • Manage Azure Blob data storage
      • Manage S3 credentials
      • Manage BaseSpace storage
      • Manage GCS storage (V37.0+)
      • Bring Your Own Bucket
      • Bring Your Own Key
    • Cases tab
      • Cases tab
      • Cases table
      • Case status
      • Browse and select cases
      • Case details
    • Creating a single case
      • Add a new case
      • Select sample type
      • Create a family tree
      • Family tree legend
      • Add a sample
      • Supported Variant callers
      • Adding patient info for the proband
      • Adding patient info for the non-proband samples
      • Secondary findings
      • Labeling a case
      • Gene list
      • Supported parental ethnicities
    • Creating multiple cases
      • Batch case upload from platform
      • CSV format requirements
      • Batch case upload via CLI
    • Reviewing a case
      • Individual case page
      • Individual case page: Top bar
      • Individual case page: Top bar
      • Candidates tab
      • Most Likely Candidates and Candidates
      • Genome Overview
      • Analysis tools tab
      • Variant table columns
      • Variant table
      • Variant search
      • Multiselection of variants and bulk actions (34.0+)
      • Download variants
      • Manually add variants to a delivered case
      • Filters/Presets panel
      • Filters
      • Presets
      • Preset groups
      • Variant Type Filters
      • Variant Effect Filters
      • Quality Filters
      • Polymorphism Filters
      • Gene Filters
      • Phenomatch Filters
      • Inheritance Filters
      • Zygosity Filters
      • User Filters
      • Evidence page
      • Phenotypic match strength
      • Lab tab
      • Versions tab
      • Editing an existing case
      • Finalizing a case
      • Clinical Report
      • Reflex genetic testing
      • Variant zygosity notations
      • STR calling and interpretation
    • Variant page
      • Variant page
      • Variant page top bar
      • Variant tagging widget
      • Variant activity panel
      • Desktop apps panel
      • Clinical Significance section
      • Summary section
      • Quality section
      • Visualization section
      • Population Statistics section
      • Related Cases section
      • CNV overlap percentage
      • Evidence section
      • ACMG SNV Classification wizard
      • Logic behind ACMG classification of SNVs
      • ACMG CNV Classification wizard
      • Variant page sidebar (2.29+)
    • Variant visualization setup
      • Enabling visualization for a VCF case
      • Integration between emedgene and desktop IGV
      • Loading alignment files to your desktop IGV (32.0+)
    • Analyze Network
      • Analyze Network Setup
      • Network sharing configuration
      • Case subject consent for extended sharing
      • Public vs Private network
      • Create a network
      • Set network data sharing policy
      • Leave a network
      • Delete a network
    • Settings
      • My settings
      • Management
      • User Management
      • Network
      • Organization Settings (33.0+)
    • Integrations
      • API Beginner Guide
      • Advanced API Implementations
      • API Key Generation
      • BSSH Integration
      • ICA Integration
      • Webhook Integration
  • Emedgene Curate Manual
    • Curate overview
      • Curate overview
      • Emedgene Applications menu
      • Curate navigation panel
      • Genome assemblies supported by Curate
    • Curate Variants
      • Curate Variants overview
      • Curate Variant table
      • Curate Variant page
      • How to add a variant to Curate
      • Curate Variant annotations in the case
    • Curate Genes (2.28+)
      • Curate Genes overview
      • Curate Gene table
      • Curate Gene page
      • How to add a gene to Curate
    • Import Curate annotations to the case (30.0+)
      • Import Curate Variant annotations to the case (30.0+)
      • Import Curate Gene annotations to the case (30.0+)
  • Frequently Asked Questions
    • All FAQ
      • Which browser should I use with Emedgene?
      • Emedgene annotations and update frequency
      • How do I use developer tools to collect logs?
      • Can I analyze Illumina Complete Long Reads in Emedgene?
      • How do I prepare VCF files generated by DRAGEN MANTA to be used as input for Emedgene?
      • Source of gnomAD data for small variants on GRCh38
      • How are MNVs handled on the platform?
      • Support for gene lists with up to 10,000 genes
      • Genomic Regions by Case Type
      • How do I analyze mtDNA variants?
      • Can I use exome data for CNV detection?
      • How does joint calling work on Emedgene?
      • What is the required format for a BED file defining a kit?
      • Which reference genomes can I use?
      • How do I move between organizations?
      • How do I check the version of my environment?
      • "Failed to generate report". What should I do?
      • How do I prepare VCF files generated by Dragen STR (ExpansionHunter) to be used as input?
      • How does Emedgene Analyze prioritize transcripts?
      • How does Emedgene Analyze merge variants from different sources?
      • Performance issue troubleshooting
      • How does Emedgene calculate variant effect and severity ?
      • How to I prepare metrics files generated by DRAGEN to be used as input for Emedgene
      • How are timekeeping and log timestamps kept accurate and consistent?
  • Release Notes
    • Workbench & Pipeline Updates
      • New in Emedgene V37.0 (February 20, 2025)
        • V37 Patches
      • New in Emedgene V36.0 (October 8 2024)
        • V36 Patches
      • New in Emedgene V35.0 (May 22nd 2024)
        • V35 Patches
      • New in Emedgene V34.0 (January 28th 2024)
        • V34 Patches
      • New in Emedgene V33.0 (September 6th 2023)
        • V33 Patches
      • New in Emedgene V32.0 (June 8th 2023)
        • New pipeline 32 (June 8th 2023)
        • V32 Patches
      • More release notes
        • New in emedgene 31 (March 1st 2023)
        • New in emedgene 30 (January 8th 2023)
        • New in emedgene 2.29 (August 25 2022)
        • New pipeline 5.29 (May 1st 2022)
        • New in emedgene 2.28 (May 1 2022)
        • New in emedgene 2.27 (March 7, 2022)
        • New in emedgene 2.26 (Dec 14, 2021)
        • New in emedgene 2.24-2.25 (Aug 11, 2021)
        • New in emedgene 2.23 (Jun 15, 2021)
        • New in emedgene 2.19-2.22 (Apr 8, 2021)
        • New in emedgene 2.16-2.19 (Dec 7, 2020)
        • New in emedgene 2.12-2.16 (Oct 18, 2020)
    • Knowledgebase Updates
      • 2025
        • Variant Databases (March 30th 2025)
        • Zoidberg 77 (March 17th 2025)
        • Zoidberg 76 (February 3rd 2025)
        • Zoidberg 75 (January 6th 2025)
      • 2024
        • Variant Databases (December 8th 2024)
        • Zoidberg 74 (December 2nd 2024)
        • Zoidberg 73 (October 21th 2024)
        • Variant Databases (September 22nd 2024)
        • Zoidberg 72 (September 10th 2024)
        • Variant Databases (July 21st 2024)
        • Zoidberg 71 (July 24th 2024)
        • Zoidberg 70 (June 3rd 2024)
        • Zoidberg 69 (April 19th 2024)
        • Variant Databases (April 9th 2024)
        • Zoidberg 68 (March 18th 2024)
        • Variant Databases (February 5th 2024)
        • Zoidberg 67 (January 28th 2024)
        • Variant Databases (January 5th 2024)
      • 2023
        • Zoidberg 66 (December 24th 2023)
        • Variant Databases (December 3rd 2023)
        • Zoidberg 65 (November 21th 2023)
        • Variant Databases (November 5th 2023)
        • Zoidberg 64 (October 24th 2023)
        • Variant Databases (October 8th 2023)
        • Zoidberg 63 (September 18th 2023)
        • Variant Databases (September 5th 2023)
        • Zoidberg 62 (August 23th 2023)
        • Zoidberg 61 (August 16th 2023)
        • Variant Databases (August 6th 2023)
        • Zoidberg 60 (July 30th 2023)
        • Variant Databases (July 2nd 2023)
        • Zoidberg 59 (June 18th 2023)
        • Variant Databases (June 4th 2023)
          • Variant Databases (May 7th 2023)
        • Zoidberg 58 (May 21th 2023)
        • Zoidberg 57 (April 16th 2023)
        • Variant Databases (April 2nd 2023)
        • Zoidberg 56 (March 19th 2023)
        • Variant Databases (March 11th 2023)
        • Zoidberg 55 (February 19th 2023)
        • Zoidberg 54 (January 16th 2023)
    • Change log
      • Change log pipeline v34
      • Change log pipeline 31
      • Change log workbench 31
      • Change log pipeline 30
      • Change log workbench 30
      • Change log workbench 2.29
      • Change log pipeline 5.29
      • Change log workbench 2.28
  • Legal
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  1. Release Notes
  2. Workbench & Pipeline Updates
  3. New in Emedgene V33.0 (September 6th 2023)

V33 Patches

PreviousNew in Emedgene V33.0 (September 6th 2023)NextNew in Emedgene V32.0 (June 8th 2023)

Last updated 10 months ago

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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 . See release notes for detail.


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.


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.

v32.4