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• Introduction
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Methods and tools
  • Methods
    • Trimming
    • Readmapping
    • Deduplication
    • Local realignment
    • Structural variant detection
    • UMI grouping
    • Germline variant detection
    • Somatic variant detection
    • Tumor normal variant detection
    • Limitations
  • Tools
    • LightSpeed Fastq to Germline Variants
      • LightSpeed Fastq to Germline Variants outputs
    • LightSpeed Fastq to Somatic Variants
      • LightSpeed Fastq to Somatic Variants outputs
    • LightSpeed Fastq to Somatic Variants Tumor Normal
      • LightSpeed Fastq to Somatic Variants Tumor Normal outputs
    • Report
• Template Workflows
  • General Template Workflows
    • Fastq to Annotated Germline Variants
      • Outputs from Fastq to Annotated Germline Variants
    • Fastq to Annotated Germline Variants with Coverage Analysis
      • Outputs from Fastq to Annotated Germline Variants with Coverage Analysis
    • Fastq to Annotated Somatic Variants
      • Outputs from Fastq to Annotated Somatic Variants
    • Fastq to Annotated Somatic Variants with Coverage Analysis
      • Outputs from Fastq to Annotated Somatic Variants with Coverage Analysis
    • Fastq to Annotated Somatic Variants (Tumor Normal)
      • Outputs from Fastq to Annotated Somatic Variants (Tumor Normal)
    • Fastq to Annotated Somatic Variants (Tumor Normal) with Coverage Analysis
      • Outputs from Fastq to Annotated Somatic Variants (Tumor Normal) with Coverage Analysis
    • Fastq to Germline CNV Control
      • Outputs from Fastq to Germline CNV Control
    • Fastq to Somatic CNV Control
      • Outputs from Fastq to Somatic CNV Control
  • Template Workflows - QIAseq Targeted DNA
    • QIAseq Fastq to Annotated Germline Variants
      • Outputs from QIAseq Fastq to Annotated Germline Variants
    • QIAseq Fastq to Annotated Somatic Variants
      • Outputs from QIAseq Fastq to Annotated Somatic Variants
    • QIAseq Fastq to Germline CNV Control
      • Outputs from QIAseq Fastq to Germline CNV Control
    • QIAseq Fastq to Somatic CNV Control
      • Outputs from QIAseq Fastq to Somatic CNV Control
  • Template Workflows - QIAseq Targeted DNA Pro
    • QIAseq Pro Fastq to Annotated Germline Variants
      • Outputs from QIAseq Pro Fastq to Annotated Germline Variants
    • QIAseq Pro Fastq to Annotated Somatic Variants
      • Outputs from QIAseq Pro Fastq to Annotated Somatic Variants
    • QIAseq Pro Fastq to Germline CNV Control
      • Outputs from QIAseq Pro Fastq to Germline CNV Control
    • QIAseq Pro Fastq to Somatic CNV Control
      • Outputs from QIAseq Pro Fastq to Somatic CNV Control

Structural variant detection

The LightSpeed Fastq to Germline Variants and LightSpeed Fastq to Somatic Variants tools can infer tandem duplications and inversions from unaligned ends during the realignment step.

This works by

1. Identifying breakpoints where multiple reads share a common unaligned end at the same position.
2. Aligning the sequence of identified breakpoints (unaligned end and upstream sequence) to each other and the reference sequence up or downstream of the breakpoints to find likely matches.

Tandem duplications can be detected from pairs of breakpoints that are within 1000 base pairs of each other.

Inversions can be detected from pairs of breakpoint on the same chromosome. The tool only reports the longest possible inversion when multiple breakpoints support similar inversions.

Default inversion detection requires breakpoint support from both sides of the breakpoint, but the option Lenient inversion detection allows detection of inversions where each breakpoint is only supported by reads from one side of the breakpoint. Lenient inversion detection can be relevant when analyzing targeted data. Enabling lenient variant detection can lead to detection of more false positive inversions, and is also likely to increase the processing time.

Tandem duplications are reported in the variant track. Tandem duplications that are inferred fom unaligned ends are annotated with Yes in the variant track column Inferred from unaligned ends. Identified inversions are reported in the inversions track.

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