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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
    • Primer trimming
    • Germline variant detection
    • Somatic variant detection
    • Tumor normal variant detection
    • Batching
    • 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 from LightSpeed Fastq to Variants tools
    • Calculate TMB Score (LightSpeed)
    • Copy Number Variant Detection (WGS) (beta)
      • Copy Number Variant Detection (WGS) (beta) outputs
• 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
• Bibliography

Copy Number Variant Detection (WGS) (beta) outputs

Copy Number Variant Detection (WGS) (beta) produces a track containing detected CNVs and a report.

The track contains all detected CNVs with the CNV region and the following information:

• Length The length of the CNV in base pairs.
• Median read counts per window The median read count per window that is part of the CNV.
• Copy Number The predicted copy number of the CNV.
• Score A score reflecting the probability of the CNV being a true event.
• Consequence The consequence of the detected CNV, i.e. "Gain" or "Loss".

The report contains the following sections:

• Summary A summary table containing general information about the sample, the window size and the identified CNVs.
• References A table listing each of the analyzed chromosomes together with the number of reads mapped to the chromosome and the average coverage.
• CNVs per chromosome A table listing each of the analyzed chromosomes together with the number of losses and gains and the number of positions affected by gains and losses.
• Visualization of copy number variations A plot depicting identified CNVs on the chromosomes.
• Chromosome window read count distributions Plot of the normalized mean read count per window versus the standard deviation for the read count per window. Each chromosome is represented by one dot. The selected cluster is dark blue, and chromosomes that are not part of the cluster are light blue. A plus sign is positioned at the center of the selected cluster. The mean coverage at the center of the selected cluster is defined as the expected coverage for a diploid region.
• Size distribution A table summarizing the sizes of identified CNVs.
• Coverage per window and identified CNVs relative to chromosome average A section containing a plot for each chromosome. The plots show normalized read counts per window versus chromosome position. Identified CNVs and masked regions are also illustrated.

  The plots contain one dot for each window, but dots may be collapsed if they cannot be visually discerned.

  Per default, the Y-axis is scaled to fit 95% of all dots; however, identified CNVs will always be included and this can result in more than 95% of all dots being visible in the plot.

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