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• Introduction
  • Overview of CLC LightSpeed Module
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Methods
  • Trimming
    • Quality trimming
    • Adapter trimming
  • Generating read mappings
    • Readmapping - short reads
      • Indexing
      • Read mapping and read pairs
    • Readmapping - long reads
      • Indexing
      • Read mapping
    • Remove ligation artifacts
    • Deduplication
    • Local realignment
    • UMI grouping
      • Definitions
    • Primer trimming
  • Structural variant detection
  • Variant detection
    • Germline variant detection
    • Somatic variant detection
    • Tumor normal variant detection
    • Variant detection using target regions
  • Batch processing
  • Compatibility with CLC Genomics Workbench tools
  • 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
    • Summary
    • Input read QC
    • Quality trimming
    • Adapter trimming
    • Mapping statistics
  • LightSpeed Long Reads to Germline Variants (beta)
    • LightSpeed Long Reads to Germline Variants (beta) outputs
    • Genotype track
      • Getting started
      • Locus table
      • Allele table
      • Track view
      • Header view
      • Differences between genotype tracks and variant tracks
      • VCF compatibility
      • Genotype track filtering and annotation
  • Report from LightSpeed Long Reads to Germline Variants
    • Summary
    • Input read QC
    • Quality trimming
    • Mapping statistics
  • Calculate TMB Score (LightSpeed)
  • Copy Number Variant Detection (WGS)
    • Copy Number Variant Detection (WGS) outputs
  • LightSpeed Utility Tools
    • Convert Genotype Track to Variant Track (beta)
    • Import VCF to Genotype Track (beta)
    • Genotype Track Amino Acid Changes (beta)
  • Prepare Sequencing Data
    • LightSpeed Demultiplex QIAseq Long Reads
      • LightSpeed Demultiplex QIAseq Long Reads outputs
  • Export genotype track to VCF
  • Export genotype track allele table to CSV
• Template Workflows
  • General Template Workflows
    • Fastq to Germline Variants (WGS)
      • Outputs from Fastq to Germline Variants (WGS)
    • Fastq to Germline Variants (WES)
      • Outputs from Fastq to Germline Variants (WES)
    • Fastq to Somatic Variants (WGS)
      • Outputs from Fastq to Somatic Variants (WGS)
    • Fastq to Somatic Variants (WES)
      • Outputs from Fastq to Somatic Variants (WES)
    • Fastq to Somatic Variants (Tumor Normal) (WGS)
      • Outputs from Fastq to Somatic Variants (Tumor Normal) (WGS)
    • Fastq to Somatic Variants (Tumor Normal) (WES)
      • Outputs from Fastq to Somatic Variants (Tumor Normal) (WES)
  • Template Workflows - QIAseq Targeted DNA
    • QIAseq Fastq to Germline Variants
      • Outputs from QIAseq Fastq to Germline Variants
    • QIAseq Fastq to Somatic Variants
      • Outputs from QIAseq Fastq to Somatic Variants
  • Template Workflows - QIAseq Targeted DNA Pro
    • QIAseq Pro Fastq to Germline Variants
      • Outputs from QIAseq Pro Fastq to Germline Variants
    • QIAseq Pro Fastq to Somatic Variants
      • Outputs from QIAseq Pro Fastq to Somatic Variants
  • Template Workflows - QIAseq xHYB
    • QIAseq xHYB CGP Fastq to Somatic Variants
      • Outputs from QIAseq xHYB CGP Fastq to Somatic Variants
    • QIAseq xHYB CGP cfDNA Fastq to Somatic Variants
      • Outputs from QIAseq xHYB CGP cfDNA Fastq to Somatic Variants
  • Template Workflows - QIAseq xHYB Long Read
    • QIAseq xHYB Long Reads to Germline Variants (ONT) (beta)
      • Outputs from QIAseq xHYB Long Reads to Germline Variants (ONT) (beta)
    • QIAseq xHYB Long Reads to Germline Variants (PacBio) (beta)
      • Outputs from QIAseq xHYB Long Reads to Germline Variants (PacBio) (beta)
    • Guide to changing reference data
  • Template Workflows - Twist
    • Twist CGP Fastq to Somatic Variants
      • Outputs from Twist CGP Fastq to Somatic Variants
• Bibliography

Outputs from QIAseq xHYB CGP Fastq to Somatic Variants

The QIAseq xHYB CGP Fastq to Somatic Variants template workflow can produce a number of outputs depending on the settings that are chosen in the Specify workflow path wizard step.

Sample analysis outputs that are available when Analysis options is set to Analyze sample or Analyze sample and create CNV control:

• Variants A variant track () with the annotated variants.

• LightSpeed Report A report () summarizing details of each analysis step performed by the LightSpeed Fastq to Somatic Variants tool.

• Mapped UMI Reads A read mapping track () with the mapped UMI reads.
• Coverage Report A report () summarizing coverage.
• Per Region Statistics Track A track () providing coverage information per target region. The Coverage Report and the Per Region Statistics Track are produced by QC for Targeted Sequencing.
• Amino Acid Track A track () providing a graphical representation of identified amino acid changes. The Amino Acid Track is produced by Amino Acid Changes.
• ID SNP variants (). A track showing the detected variants at ID SNP positions. Note that only ID SNP positions where the detected variant is different from the reference genome are shown.

  This output can be used to compare different samples to assess whether they come from the same patient:

  1. For each read mapping, generate a graph track using Create Mapping Graph. Ensure that the same type of reads used for variant calling are included.
  2. Use the "Use upper threshold" option in Identify Graph Threshold Areas to detect regions of low coverage in each sample.
  3. Use Merge Annotation Tracks to combine the identified low coverage regions.
  4. For each sample, use the "Remove overlapping annotations" option in Filter Based on Overlap to exclude SNPs located in low coverage regions.
  5. Use Identify Shared Variants to compare ID SNPs between samples. The output will include a "Sample count" indicating how many samples contain each SNP.
  6. Finally, use Filter on Custom Criteria to retain only the ID SNPs that are not present in all samples. Use the filter criterion "Sample count < n", where n is the number of samples (typically 2).

  The output will contain only the ID SNPs that differ between the samples. Based on this, you can evaluate the degree of similarity between the samples to assess if they are likely to come from the same patient.

• Genome Browser View A track list () containing the Reference sequence, the Per Region Statistics Track, the Mapped UMI Reads, Variants, Gene-level CNVs and Fusion Genes (if detection enabled), the Genes, mRNA, CDS and the Amino Acid Track.
• Sample Report A report () that contains compiled QC metrics from other reports and provides an overview of a given sample. The report contains a quality control section reflecting the summary items specified in the Create Sample Report wizard step.

• Additionally, if CNV detection is enabled:
  • CNV Results Report A report () providing an overview of identified CNVs.
  • 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.
  • Target-level CNV Track An annotation track () providing CNV results per target.

  The results are produced by Copy Number Variant Detection (Targeted), see Copy Number Variant Detection for details.

• Additionally, if fusion detection is enabled:
  • Fusion report (): A report summarizing the identified fusions.
  • Fusion Unaligned Ends (): The unaligned ends mapped to the reference genome.
  • Fusion Genes (): A track containing the breakpoints on the reference genome of detected fusions that have passed all relevant filters.

  The results are produced by Detect Fusion Genes from DNA, see Detect Fusion Genes from DNA for details.

• Additionally, if MSI detection is enabled:
  • MSI report () A report containing the MSI status of the sample and the stability of the individual loci.
  • MSI Loci Track () An annotation track containing the MSI loci annotated with predicted stability.

  The results are produced by Detect MSI Status, see Detect MSI Status for details.

• Additionally, if TMB calculation is enabled:
  • TMB report () A report containing the TMB score and confidence values.
  • TMB Somatic Variants () Filtered variants that are included in the TMB score calculation.

  The results are produced by Calculate TMB Score (LightSpeed), see Calculate TMB Score (LightSpeed) for details.

• Additionally, if Prepare for QCI Interpret Upload is enabled:
  • QCI Interpret report () A report containing the sample analysis results in a form that allows for later upload to QCI Interpret.

  The report is produced by Prepare QCI Interpret Upload, see Prepare QCI Interpret Upload for details.

CNV control output that is available when Analysis options is set to Create CNV control or Analyze sample and create CNV control:

• Coverage table () Contains the coverage for every target region position and can be used as control in Copy Number Variant Detection (Targeted). See Coverage table for details.

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