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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

Outputs from Fastq to Annotated Somatic Variants with Coverage Analysis

The Fastq to Annotated Somatic Variants with Coverage Analysis template workflow produces the following outputs:

• Somatic Variants The variant track () with the annotated variants.
• Inversions An annotation track () providing the called inversions.
• Ignored Regions An annotation track () providing regions where it was not possible to detect variants due to high complexity among the initial variants being tested.
• LightSpeed Report A report () summarizing details of each analysis step performed by the LightSpeed Fastq to Somatic Variants tool.
• Genome Browser View A track list () containing the Somatic Variants, the Ignored Regions, the Amino Acid Track, the Target regions, the Target Region Statistics Track, the Gene-level CNV Track, the Read Mapping as well as the Reference sequence and the Genes, mRNA and CDS tracks.
• Read Mapping A read mapping track ().
• Amino Acid Track A track () providing a graphical representation of identified amino acid changes.
• CNV Results Report A report () providing an overview of identified CNVs.
• Target-level CNV Track An annotation track () providing CNV results per target.
• Gene-level CNV Track An annotation track () providing CNV results per gene.
• Region-level CNV Track An annotation track () providing CNV results per region, where regions are formed from adjacent targets with similar CNV states.
• Coverage Report A report () summarizing coverage.
• Target Region Statistics Track A track () providing coverage information per target region.
• Gene Coverage Track A track () providing coverage information per gene.
• Sample Report A report () containing essential information from all reports produced by the workflow. For further details, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report.html.

The Amino Acid Track is produced by Amino Acid Changes (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Amino_Acid_Changes.html).

The CNV Results Report, and the Target, Gene and Region-level CNV Tracks are produced by Copy Number Variant Detection (CNVs) (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Copy_Number_Variant_Detection.html).

The Coverage Report, Target Region Statistics Track and the Gene Coverage Track are produced by QC for Targeted Sequencing (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Targeted_Sequencing.html).

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