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
  • New CNV Analysis Tools
  • New Gene Filters: LoF Genes, Established HI/TS Genes
  • New Quality Filter: Bin Count
  • Extended CNV Quality Metrics
  • UI & Workflow Improvements
  • Variant page redesign: brand new Summary section andupdated Quality section
  • Variant type filter & column
  • Full control over your gene lists
  • Restricted access to Finalized Case status

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  1. Release Notes
  2. Workbench & Pipeline Updates
  3. More release notes

New in emedgene 2.19-2.22 (Apr 8, 2021)

PreviousNew in emedgene 2.23 (Jun 15, 2021)NextNew in emedgene 2.16-2.19 (Dec 7, 2020)

Last updated 2 months ago

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New CNV Analysis Tools

New Gene Filters: LoF Genes, Established HI/TS Genes

Two new CNV filters will help you focus on the genes that are most likely to be pathogenic:

  • LoF Genes will present all genes with a gnomAD pLI≥0.9;

  • Established HI/TS Genes filter will only return variants genes with an HI/TS score of 3.

Both are available under and can be added to your preset filters.

New Quality Filter: Bin Count

Extended CNV Quality Metrics


UI & Workflow Improvements

Variant page redesign: brand new Summary section andupdated Quality section

To change the sample in review for the particular variant, click on the corresponding icon in the family tree.

If you've read this far, here is a bonus insider tip! 🤫

Variant type filter & column

Full control over your gene lists

Restricted access to Finalized Case status

If you’d like to focus on high-quality CNVs, you can now set a minimum bin count of 1, 5, 10, 25, 50, 100 or 500 in CNV Bin Count filter. The filter appears under in Advanced mode.

for CNVs got updated! For each sample, you can now see copy number, CNV quality, size, and bin count.

The now features a clear that spotlights essential variant information - saving you precious clicks! If after the first glance you feel like diving deeper into the variant details - proceed to other Variant page sections below.

We redesigned : it has a slightly different style,

Did you know that you can view the for any tagged variant? We redesigned the See evidence button on the to make it pop!

Piping hot at your command! Ready to filter variants by type (SNV, Indel, DEL, DUP). Additionally, variant type is shown in the variant table.

Administrators of your account now have total control over and can create and edit them in .

The Finalized locks the case to prevent further changes to interpretation notes, ACMG tags, variant tags, pathogenicity and case-level interpretations.

Starting from this version, access to requires a dedicated , so the organization's manager can restrict access to a specific set of users.

Quality Filters
Quality section
Variant page
Summary section
Quality section
Evidence page
Evidence section
Variant Type Filters
gene lists
Settings
Case status
finalizing a case
role
Gene Filters
New CNV Analysis Tools
New Gene Filters: LoF Genes, Established HI/TS Genes
New Quality Filter: Bin Count
Extended CNV Quality Metrics
UI & Workflow Improvements
Variant page redesign: brand new Summary section andupdated Quality section
Variant type filter & column
Full control over your gene lists
Restricted access to Finalized Case status