LogoLogo
Illumina KnowledgeIllumina SupportSign In
  • Home
  • Overview
    • Welcome
    • What's New
      • Cloud Software Update
      • Local Software Update
  • Configure
    • Configuration
      • Custom Case Data
      • Pipeline and QC Configuration
      • Preferred Transcripts
      • Custom Annotations
      • Disease Configuration
      • Variant Filters
      • Variant Flag Groups
      • Actionability Classifications
      • Report Templates
        • Customizations
      • Report Automation
      • Test Definitions
      • Data Upload
        • Data Upload from User Storage (Connected Insights - Cloud and Connected Insights - Local)
        • Data Upload from ICA or BSSH (Connected Insights - Cloud)
        • Supported Pipelines
          • DRAGEN TruSight Oncology 500 Analysis Software v2.6.0 (with HRD)
          • DRAGEN TruSight Oncology 500 Analysis Software v2.6.0
          • DRAGEN TruSight Oncology 500 Analysis Software v2.5.3 (with HRD)
          • DRAGEN TruSight Oncology 500 Analysis Software v2.5.3
          • DRAGEN TruSight Oncology 500 Analysis Software v2.5.2 (with HRD)
          • DRAGEN TruSight Oncology 500 Analysis Software v2.5.2
          • DRAGEN TruSight Oncology 500 Analysis Software v2.1.1 (with HRD)
          • DRAGEN TruSight Oncology 500 Analysis Software v2.1.1
          • DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.1
          • DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.0
          • DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.5.0
          • DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.1.1
          • DRAGEN Amplicon v4.3
          • DRAGEN Amplicon v4.2
          • DRAGEN Amplicon v4.1
          • DRAGEN RNA v4.3
          • DRAGEN RNA v4.2
          • DRAGEN RNA v4.1
          • DRAGEN Enrichment v4.3
          • DRAGEN Enrichment v4.2
          • DRAGEN Enrichment v4.1
          • DRAGEN for Illumina cfDNA Prep with Enrichment v4.0.3
          • DRAGEN Somatic Whole Genome v4.3
          • DRAGEN Somatic Whole Genome v4.2
          • DRAGEN Somatic Whole Genome v4.1
          • TruSight Tumor 170 Local App v2.0.1
          • Local Run Manager TruSight Tumor 15 Analysis Module v2.1
        • Custom Pipeline Configuration
          • VCF Input Requirement
          • TMB, MSI, GIS Input Requirement
        • Custom Case Data Upload
    • Upload Assertions
    • Local Installation Guide
      • Overview
      • Prerequisites
      • Download Connected Insights Package
      • Install Connected Insights Software
      • Install License File
      • Sign In to Connected Insights
      • Installation Status Messages
      • Local Configurations
      • Administration Console (Connected Insights - Local)
      • Configure External Storage (Connected Insights - Local)
  • Manage cases
    • Cases Page
    • Cases List
      • Case Metadata Upload
  • Interpret and report
    • Case Page
    • Case Details
      • Merge Cases
    • Overview Tab
      • Classification & Risk Stratification Prediction
    • Visualize Tab
    • Variants Tab
      • Modify Columns
      • Apply Variant Filters
        • Filter by Variant Category
        • Variant Details Filters
        • Variant Quality Filters
        • Functional Impact Filters
        • Disease Association Filters
        • Variant Frequency Filters
        • Flags Filter
        • Filtering Logic
      • IGV Visualizations
    • Lab QC Tab
    • Report Tab
    • View Biomarker Details
      • Biological Classification
      • Actionability
      • Clinical Trials
      • Oncogenicity Prediction
      • Visualize
      • Variant Overview
      • Gene Overview
      • Cancer Datasets
      • Computer Predictors
      • Population
    • Interpret a Biomarker
      • Create Clinical Trials
      • Create Gene Descriptions
      • Manage Assertions
    • Variant Transcripts
    • Add Variant
  • Resources and References
    • Glossary
    • APIs
      • Ingest Cloud Analysis Data API (Connected Insights - Cloud Only)
      • Case APIs
      • Report APIs
      • Audit Log APIs
    • Troubleshooting
      • Overview
      • Audit Log
      • Data Backup (Connected Insights - Local)
      • Software Errors and Corrective Actions
      • How To
      • Technical Assistance
    • Pricing and Usage
    • Security and Compliance
    • Release Notes
Powered by GitBook
On this page
  • Create a new Custom Annotation file
  • Upload a new Custom Annotation file
  • Download an existing Custom Annotation file
  • Annotating Variants

Was this helpful?

Export as PDF
  1. Configure
  2. Configuration

Custom Annotations

PreviousPreferred TranscriptsNextDisease Configuration

Last updated 19 hours ago

Was this helpful?

Custom Annotations allow you to annotate custom attributes (labels, scores, and population frequency) to variants or variants within a genomic region.

Create a new Custom Annotation file

  1. Select the icon (gear icon) in the top right area of the screen.

  2. Select the Test Components tab.

  3. Navigate to Custom Annotations.

  4. Select New.

  5. Download the attached template.

  6. Edit the file with the desired annotations. Refer to .

The supported data categories for custom annotation in Connected Insights are as follows:

  • Filter: String labels

  • Score: Numeric values

  • AlleleFrequency: Allele frequency for population frequency data

Upload a new Custom Annotation file

  1. Select the icon (gear icon) in the top right area of the screen.

  2. Select the Test Components tab.

  3. Navigate to Custom Annotations.

  4. Select New.

  5. Upload the file.

Download an existing Custom Annotation file

  1. On the top toolbar, select Configuration, and then select the Test Components tab.

  2. Select the Custom Annotations section.

  3. Select the desired custom annotation.

  4. Select Download.

Annotating Variants

After a custom annotation is added to a and cases are ingested using the test definition, the variants will be annotated. The annotations can then be and on.

When matching annotations for large variants (structural variants and copy number variants), by default Annotation Overlap (measured as the total overlap divided by the length of the annotation) of >= 0.75 is used, but can be changed to Reciprocal Overlap (measured as the total overlap divided by either the length of the annotation or the length of the variant, whichever is larger) by specifying Reciprocal Overlap in the Description column for the annotation. For more information, refer to .

Configuration
Custom Annotation File Format
Configuration
Custom Annotation File Format
Test Definition
viewed
filtered