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
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      • 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
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      • 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
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    • Settings
      • My settings
      • Management
      • User Management
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      • Organization Settings (33.0+)
    • Integrations
      • API Beginner Guide
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  • 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
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On this page
  • Release Highlights
  • Pipeline: Support for DRAGEN 4.2 Release
  • Limitations
  • Platform: Organization Settings. New self-serve features available to customers
  • i. Select your own URLs from the available URLs in your domain
  • ii. Select a platform version for your organization from officially released versions
  • iii. Set your own case identifier to display on the case and variant page
  • IV. Improved BED validation errors
  • Limitations
  • Platform: Workflow enhancements
  • Support for ACMG Secondary Findings v3.2
  • Edit a case label after case creation from the UI
  • New export capabilities
  • Limitations
  • Fixed issues
  • Known issues

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  1. Release Notes
  2. Workbench & Pipeline Updates

New in Emedgene V33.0 (September 6th 2023)

PreviousV34 PatchesNextV33 Patches

Last updated 2 months ago

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Patches
Date

Feb 18th, 2024

Jan 14th, 2024

Release Highlights

  1. - New self-serve features available to customers

Emedgene customers can select their preferred version out of any of the past 5 releases. Customers on v29.0 should select an upgrade path at this time.

The software release includes the following components, which can be selected independently:

  • Platform 33

  • Pipeline 33

Pipeline: Support for DRAGEN 4.2 Release

All supported DRAGEN callers can now be run with DRAGEN 4.2, for customers starting from FASTQ or VCF.

DRAGEN 4.2 includes enhanced multigenome (graph) reference and Machine Learning (ML) models that improve small variant calling accuracy. Emedgene supports the new graph and ML while maintaining backward compatibility for customers on previous DRAGEN versions.

Improved CNV calling accuracy achieved through joint CNV/SV detection is available for customers starting from VCF (FASTQ support coming in 34.0). In order to minimize duplication, SV variants that are not merged with CNVs are removed from the CNV_SV VCF, and are ingested separately via the SV VCF.

Supported DRAGEN 4.2 outputs in 33.0:

Limitations

  • Discrepancies between DRAGEN callers supported from VCF and FASTQ, where some are only supported from FASTQ and some from VCF, will be addressed in Emedgene 34.0 (Q4 23).

  • Not all DRAGEN 4.2 callers are supported.

  • High sensitivity caller will be supported in 34.0.

  • Additional targeted callers will be supported in mid-2024 with the release of DRAGEN 4.3.


Platform: Organization Settings. New self-serve features available to customers

In 33.0 we’ve added the following self-serve capabilities:

i. Select your own URLs from the available URLs in your domain

Customers on ILMN clouds can now select their preferred URLs. It takes 1-15 minutes for URL changes to go live.

ii. Select a platform version for your organization from officially released versions

This feature is available for both Emedgene and Illumina cloud customers. It takes 1-15 minutes for changes to go live.

Note:

  1. This is available only on 33.0 and up. If you select a previous version the feature will disappear from your organization settings, and you will need to contact support to change platform versions.

iii. Set your own case identifier to display on the case and variant page

Emedgene by default displays the EMGXXXXXXXXX case identifier. Customers can now choose to display the proband ID instead. The proband ID has a visible 13-character limitation, and the remaining characters will be visible on hover.

Candidate page displaying a proband ID:

Variant page displaying a proband ID:

IV. Improved BED validation errors

When attaching a BED file to a kit in the Management tab, the system will generate clear and actionable error messages for any exceptions that may occur.

Limitations

  • Proband ID field is limited to 13 characters.

  • Changing a preferred URL or a platform version takes 1-15 minutes to go live.


Platform: Workflow enhancements

Support for ACMG Secondary Findings v3.2

For the XAI, when a user selects to receive secondary findings, we will apply the v3.2 gene list (requires pipeline 33).

Edit a case label after case creation from the UI

New export capabilities

  • Export/report on the gene list associated with the case HPO terms. This gene list is produced with the Phenomeld phenotypic match algorithm. The capability was added in 32.0 but now customers can include the gene list in their report.

Limitations

  • Analysis Tools | Sort by phenomatch score and tags is not yet available

  • Curate | Some HGVS p-values not accepted yet, discrepancy between Curate and Analyze


Fixed issues

  • ClinVar sanity check fails case if there are no known variants in ChrY with wrong message. Cases will still fail but with the correct error message.

  • Variant Page | Fixed an issue where a manually added transcript would display twice.

  • Analysis Table | Filters | Polymorphism Filters | Fixed an issue where a filter was mislabeled Het or Het Count instead of Allele Count. No variants were missed due to this mislabeling, as the Allele Count filter is more inclusive.

  • Analysis Table | Preset Filters | Fixed bug where updated gene lists were resulting in a case incompatible error message.

  • Analysis Table | Fixed an issue where manually added variants were sorted incorrectly causing them to ‘disappear’ from the UI.

  • Add New Case, Lab Tab, Cases Sidecar | Gender changed to Sex.

  • Add New Case | Fixed a bug where users couldn’t edit cases that failed due to bad inputs.

  • Lab Tab | Fixed an issue where % mapped reads was always 0.

  • Export/Report | Fixed an issue where synonymous variants were exported with ‘%3D’ instead of ‘=’.

  • Notification | Fixed a bug where case delivery email notifications included organization parameters based on the user creating a case rather than the organization.


Known issues

  • Organization Settings | Set mandatory fields - does not work from the UI. Please contact support if you’d like to configure these fields for your account.

  • Gene Lists | Very large gene lists (>6700 genes) may return a false error message during creation, despite being successfully created.

  • Visualization is not supported for users storing VCF and CRAM on ICA V1 and BSSH. Only VCF and BAM are supported.

  • Variant Page | Visualization | Chromosome ideogram visualization is missing for mtDNA variants in VCF case run on GRCh37.

  • Variant Page | Visualization | Simple/Advanced selectors will not work for locally uploaded BAM files.

  • Variant Page | Visualization | Zoom out of BigWig/TTS displays mean data.

  • Variant Page | ACMG SNV Score | Incorrect score for mtDNA variants, although classifier behaves as expected.

  • Analysis Tools | Preset Filters | Preset containing a gene list ID will display filtered data when an organization has configured a base gene list filter.

  • Analysis Tools | ‘Last’ button on pagination does not work.

  • Candidates Page | Compound het SNV-CNV variants will not display the automated CNV classification. Workaround – view variants from analysis table.

  • Candidates | When clicking on See all candidates link, variant filters are inactivated. Workaround: Reset filters to default.

  • Candidates | SV Insertions information partially displayed. Work around: View from a preset filter.

  • Network | GRCh37<-->GRCh38 Liftover not available for older components of Network infrastructure, as a result, [Variant Page | Clinical Significance | Networks Classified] may remain erroneously empty while [Variant page | Related cases section] shows relevant information. Same gap for manually classified variants.

  • Network | Zygosity, even when set in extended sharing, may remain blank for older cases. Once you click on a case missing zygosity it will be saved for all future views.

  • Manually Added Variants | STRs -When manually adding an STR variant it cannot be tagged or reported.

  • Manually Added Variants | Users without the role can add variants but not save them. Button should be disabled.

  • ILMN Clouds | Help Center | Some links may not work. Work around: Paste the title into the help center search.

  • Add New Case | Batch Upload | Analysis Type field is not available with this version of Batch Upload, and it cannot be used to initiate the new Carrier workflow.

  • Add New Case | Create a case from case creation summary does not work, please click on top Add New Case button from cases page.

  • Reanalysis | If HPO terms were updated between analyses, the reanalysis will not automatically map previous HPO terms to new ones.

  • Lab Tab | Reanalyzed cases will show up with duplicated insufficient gene regions. Fix planned for 34.0 .

  • Lab Tab, Sidecar | Pedigree | In very large pedigrees some family members can’t be clicked to view quality.

  • Lab Tab | STR repeats number for parents does not exist, proband values displayed.

  • Curate | ILMN cloud users need to be logged in to the organization from which they are trying to access Curate.

  • API | Assign users to case fails with no error if faulty emails used.

  • API | Creation of large gene lists may return an error (due to timeout) despite the creation of the gene list.

  • Report/Export | For variants tagged as ‘Most Likely’ order is not preserved when pushing to the report. Work around – use another tag, e.g. ‘In Report’.

  • Activity | Editing interpretation paragraph yields an erroneous activity labeled reanalysis.

  • Dashboard | Diagnostic Yield includes Uncertain as Resolved.

A new Organization Settings page will enable customers to progressively control their organization settings without requesting ILMN support. To access the page: Click on the user initials or profile picture > > Organization Settings.

Note that this will not change your pipeline version, only the software platform. To change a pipeline version please contact .

Each of these new features requires a unique . Contact your support team or to add these roles to your organization.

The gene list has been updated in both the XAI and the filters.

The has also been updated to this new list of 81 genes.

can now be edited after case creation through the UI in the , in addition to the existing capability via the API. This is -based, please contact your support team or to add these to your organization.

Added CNV annotations to the mini VCF – Emedgene produces a lightly annotated VCF that is available for customers to for every case. In this version the following CNV annotations were added to this file: decipher_sv, dgv_sv, GnomAD_SV, clinvar_benign_sv, clinvar_uncertain_sv, clinvar_pathogenic_sv, clingen_benign, clingen_uncertain, clingen_pathogenic and DDD (requires pipeline 33).

Cases Page | Contact support link for failed cases does not work. Please use .

Settings
techsupport@illumina.com
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ACMG secondary findings v3.2
All ACMG genes
filter
Case labels
Cases table
role
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download
techsupport@illumina.com
Pipeline: Support for DRAGEN 4.2 Release
Platform: Organization Settings
Select your own URLs from the available URLs in your domain
Select a platform version for your organization from officially released versions
Set your own case identifier to display on the case and variant page
Improved BED validation errors
Platform: Workflow enhancements
Support for ACMG Secondary Findings v3.2
Edit a case label after case creation from the UI
New export capabilities
Fixed issues
Known issues
V33.2
V33.1