DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • DRAGEN TSO 500 Guides
    • DRAGEN TSO 500 v2.6
      • Introduction to DRAGEN TSO 500 Analysis Software v2.6.x
      • Getting Started
        • Installation of 2.6.0 on Standalone DRAGEN Server
        • Installation of 2.6.1 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • RNA Analysis Methods
        • Quality Control
        • Performance Testing
      • Troubleshooting
    • DRAGEN TSO 500 v2.5
      • Introduction to DRAGEN TSO 500 Analysis Software v2.5.x
      • Getting Started
        • Installation of 2.5.3 on Standalone DRAGEN Server
        • Installation of v2.5.4 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
          • Block List
        • Analysis Methods
          • FASTQ Generation
          • DNA Analysis Methods
          • RNA Analysis Methods
          • Quality Control
          • Performance Testing
      • Troubleshooting
  • DRAGEN TSO 500 ctDNA Guides
    • DRAGEN TSO 500 ctDNA v2.6
      • Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6
      • Getting Started
        • Installation of TSO 500 ctDNA v2.6.0 on Standalone DRAGEN Server
        • Installation of TSO 500 ctDNA v2.6.2 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 ctDNA Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
      • Analysis Output
        • DNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • Quality Control
      • Troubleshooting
  • Reference
    • Revision History
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  1. DRAGEN TSO 500 Guides
  2. DRAGEN TSO 500 v2.6
  3. Analysis Output

Combined Variant Output

File name: {Pair_ID}_CombinedVariantOutput.tsv

The combined variant output file contains the variants and biomarkers in a single file that is based on a single sample. If using pair ID, the file is based on paired DNA and RNA samples from the same individual. The output contains the following variant types and biomarkers:

  • Small variants

  • Copy number variants (CNV) (with absolute copy number when HRD Assay is run)

  • TMB

  • MSI

  • Fusions

  • Splice variants

  • GIS (when HRD Assay is run)

  • Gene-level Loss of Heterozygosity (when HRD Assay is run)

  • Large Rearrangements

The combined variant output file also contains Analysis Details and Sequencing Run Details sections. The details of each are listed in the following table:

Analysis Details
Sequencing Run Details

- Pair ID - DNA sample ID (if DNA is run) - RNA sample ID (if RNA is run)

- Library Prep Kit - Output date - Output time - Module version - Pipeline version (Docker image version #)

- Run name - Run date - DNA sample index ID (if DNA is run) - RNA sample index ID (if RNA is run) - [HRD] Sample feature - Instrument ID - Instrument control software version - Instrument type

- RTA version - Reagent cartridge lot number

Combined variant output produces small variants with blank fields in the following situations:

  • The variant has been matched to a canonical RefSeq transcript on an overlapping gene not targeted by TruSight Oncology 500.

  • The variant is located in a region designated iSNP, indel, or Flanking in the TST500_Manifest.bed file located in the Resources folder.

Variant Filtering Rules

  • Small Variants - All variants with the FILTER field marked as PASS in the hard-filtered genome VCF are present in the combined variant output.

    • Gene information is only present for variants belonging to canonical transcripts that are within the Gene Allow List–Small Variants.

    • Transcript information is only present for variants belonging to canonical transcripts that are within the Gene Allow List–Small Variants.

  • Copy Number Variants - Copy number variants must meet the following conditions:

    • FILTER field marked as PASS.

    • ALT field is <DUP or <DEL> .

  • Fusion Variants - Fusion variants must meet the following conditions:

    • Passing variant call (KeepFusion field is true).

    • Contains at least one gene on the fusion allow list.

    • Genes separated by a dash (-) indicate that the fusion directionality could be determined. Genes separated by a slash (/) indicate that the fusion directionality could not be determined.

  • Biomarkers TMB/MSI - Always present when DNA sample is processed.

  • Splice Variants - Passing splice variants that are contained on genes EGFR, MET, and AR.

  • Biomarker GIS - Present only if TruSight Oncology 500 HRD analysis is performed

  • Loss of Heterozygosity - Present only when TruSight Oncology 500 HRD is run. Loss of heterozygosity (LOH) must meet the following condition:

    • MCN field is equal to 0

  • Large Rearrangements CNV - Large Rearrangements CNVs must meet the following conditions:

    • BRCA1 or BRCA2 contains at least one affected exon.

    • ALT field is <DUP> or <LOSS> .

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