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
    • Privacy, Security & Compliance
    • Release Policy
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On this page
  • The Organization Settings page features:
  • Environment settings
  • 1. Organization URL (ILMN clouds only)
  • 2. Platform version
  • 3. Case identifier
  • 4. Default page (34.0+)
  • 5 . Analysis tools columns order (34.0+)
  • Lab Workflow settings (34.0+)
  • 1. Presets
  • 1.1. Create Preset
  • 1.2. Review logic behind the Preset
  • 1.3. Edit Preset
  • 1.4. Lock/unlock Preset
  • 1.5. Delete Preset
  • 2. Preset groups
  • 2.1. Create Preset group from existing Presets:
  • 2.1. Create Preset group from JSON file:
  • 2.3. Review contents of the Preset group (V2 and V1)
  • 2.4. Edit Preset group
  • 2.5. Hide/unhide Preset group
  • 2.6. Download Preset group file (V2 and V1)
  • 2.7. Revert *Preset group (*V1)
  • 3. Default Preset group

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  1. Emedgene analyze manual
  2. Settings

Organization Settings (33.0+)

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Last updated 2 months ago

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The Organization Settings page (33.0+) is accessible via the dropdown menu under . Note: The Organization Settings page is accessible only for users having a Manager .

The Organization Settings page features:

Environment settings

1. Organization URL (ILMN clouds only)

Associating URLs with your workgroup on ILMN Cloud

On ILMN Cloud, customers can easily associate URLs with their current workgroup by selecting from a list of predefined URL patterns. These URLs play a crucial role in organizing and accessing workgroup-specific resources.

Key Points to Remember:

  • URL Selection: You can choose from a set of predefined URL patterns.

  • Multiple Associations: A single URL can be associated with one or several workgroups.

  • Activation Time: After selecting the URL for your workgroup, please allow 1 to 15 minutes for the changes to take effect.

Need a Custom URL?

If you would like to create a new custom URL pattern within your domain, please reach out to our technical support team at for assistance.

2. Platform version

Important! If you switch to a version older than 33.0, the feature will be removed from your Organization Settings, and you will need to reach out to support for platform version changes.

3. Case identifier

By default, Emedgene displays the Case ID in the "EMGXXXXXXXXX" format*.* However, you have the choice to use the Proband ID instead. Please note that the Proband ID has a visible 13-character limitation, with the remaining characters visible upon hovering.

4. Default page (34.0+)

The default page upon entering a case can be customized. You can choose between:

5 . Analysis tools columns order (34.0+)

Lab Workflow settings (34.0+)

1. Presets

1.1. Create Preset

1.2. Review logic behind the Preset

Click on an downward arrow icon left to the Preset's name.

1.3. Edit Preset

  1. Click on the ✏️Edit icon;

  2. Make the necessary changes. Editing the Preset requires basic understanding of JSON data format;

1.4. Lock/unlock Preset

Locking the Preset prevents any user from changing it.

  1. Click on the ��Lock/Unlock icon;

  2. Click on Lock/Unlock in the popup window.

1.5. Delete Preset

  1. Click on the 🗑️Delete icon;

  2. Confirm your decision by clicking Delete in the popup window.

Note: Only unused Presets can be deleted.


2. Preset groups

In versions prior to 34.0, creating Preset groups required technical support. With 34.0+, Preset groups can be easily created by combining different Presets. Alternatively, you can upload a JSON file that defines the Presets in a Preset group. The file name and schema will be validated upon upload.

The section has two tabs:

  • V2 (new)

  • V1 (legacy)

Migrating V1 Preset groups to the improved V2 methodology

2.1. Create Preset group from existing Presets:

  1. Click on Add new;

  2. From the dropdown, select New;

  3. Enter a name for the Preset group. Note: The Preset group can't be renamed later!

  4. Select Presets to include in the Preset group. Click Add after selecting each Preset;

  5. Drag and drop Presets to change the order;

  6. Click on Save.

2.1. Create Preset group from JSON file:

  1. Click on Add new;

  2. From the dropdown, select From file;

  3. From the file browser, select a JSON file that defines a Preset group;

  4. The system will thoroughly validate the file;

  5. If validation is successful, a Preset group will be created. Any underlying Presets that are missing from your organization will be added as well.

2.3. Review contents of the Preset group (V2 and V1)

Click on an downward arrow icon left to the Preset group's name.

2.4. Edit Preset group

  1. Click on the ✏️Edit icon; 2a. Add Presets to the group as needed. Select Presets to include in the Preset group from the dropdown. Click Add after selecting each Preset; 2b. Remove Presets from the group as needed. Click on the ��Remove icon on right to the right of the Preset name. 2c. Drag and drop Presets to change the order;

  2. Click Save.

2.5. Hide/unhide Preset group

Click on the 👁️Hide/Unhide icon.

2.6. Download Preset group file (V2 and V1)

Click on the ⬇️Download icon.

2.7. Revert *Preset group (*V1)

Click on the ↩️Revert icon to undo the migration.


3. Default Preset group

  1. Click on the dropdown arrow;

  2. Select the Preset group;

  3. Click Save.

Select a platform version for your organization from the options available in your region. Please allow 1-15 minutes for changes to become active. Keep in mind that this selection will not alter your pipeline version, only the software version. To change a pipeline version please contact .

- default option;

*;

*;

.

You can customize the default order of . Just rearrange the columns by dragging and dropping them to your preferred sequence.

Here you can review and manage organization filter .

Upon clicking on Add new, you will be redirected to Analysis tools page where you can .

Click Save. The software will perform schema validation on the edited Preset. &#xNAN;Note: you can modify the Preset's content but not its name. Note: the Preset can't be edited if it's .

Here you can review and manage filter .

Here you can create (/, , , and your organization's Preset groups.

Here you can and legacy Preset groups.

Legacy Preset groups can be migrated to the new methodology via two simple steps: the Preset group JSON file in the V1 (legacy) tab, then it on the V2 (new) tab.

This is the second step in the of the V1 (legacy) Preset group, after you have the Preset group JSON file.

When you hide a Preset group, it will no longer appear in the Preset groups list offered at case creation ( ).

Note: A cannot be hidden.

This is the first step in the of the V1 (legacy) Preset group to V2 methodology. A Preset group file contains preset names and the filters used to define each Preset in JSON format.

If a V1 Preset group that has undergone is set to revert, the corresponding V2 Preset group will be deleted.

Note: If a migrated Preset group has been assigned as , it cannot be reverted.

You can set a Preset group as default. The case is assigned to the default Preset group if no Preset group is selected or the default value is selected in the Preset group selection step.

Note: A default Preset group cannot be and cannot be .

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