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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
    • 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
  • 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
• 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)
    • 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 Germline Variants
      • Outputs from QIAseq Fastq to Germline Variants
    • QIAseq Fastq to Somatic Variants
      • Outputs from QIAseq Fastq to 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 Germline Variants
      • Outputs from QIAseq Pro Fastq to Germline Variants
    • QIAseq Pro Fastq to Somatic Variants
      • Outputs from QIAseq Pro Fastq to 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
  • 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
• Bibliography

Guide to changing reference data

The QIAseq xHYB Long Reads to Germline Variants (ONT/PacBio) (beta) template workflows use the QIAseq xHYB Long Read Panels hg38 reference data set as default, but with a few workflow adjustments, it is also possible to use either of the two alternative reference data sets QIAseq xHYB Long Read Panels hg19 or QIAseq xHYB Long Read Panels T2T-CHM13v2.0.

Note: The QIAseq xHYB Long Read Hereditary Cancer Panel includes a target region for GSTT1 on chr22_KI270879v1_alt, that is not in the hg38 no alt reference sequence. To analyze that target, use hg19 or the T2T reference data set.

The hg38 reference data set includes a sequence masking track that is used as input to LightSpeed Long Reads to Germline Variants. Because there is no masking track available for hg19 or for T2T, the template workflow that is configured to be used with hg38 cannot be used with the hg19 or T2T reference data sets directly.

Follow the steps below to first create a workflow copy, and then adjust that copy to allow use of the QIAseq xHYB Long Read Panels hg19 and QIAseq xHYB Long Read Panels T2T-CHM13v2.0 reference data sets.

1. In the navigation area, right click and choose "Open Copy of Workflow" on the relevant template workflow:
   • QIAseq xHYB Long Reads to Germline Variants (ONT) (beta), see QIAseq xHYB Long Reads to Germline Variants (ONT) (beta).
   • QIAseq xHYB Long Reads to Germline Variants (PacBio) (beta), see QIAseq xHYB Long Reads to Germline Variants (PacBio) (beta).
   See Creating and editing workflows for details about opening copies of workflows.
2. In the Worklow Editor, double click on the element LightSpeed Long Reads to Germline Variants.
3. In the "Reference masking" section of the wizard step "Choose inputs":
   • Open the dialog that allows selection of a masking track. Remove the Worflow input GenomeReferenceConsortium_masking_hg38_no_alt_analysis_set track, and delete the text in the "Workflow role" text field, the text field must be empty. Press OK.
   • Then change "Masking mode" from "Exclude annotated" to "No masking". Press Finish.
4. Save the workflow to the navigation area.
5. It is now possible to run the workflow directly from the navigation area, or create a controlled version by installing it. Read the section Workflow installation for more information.
6. When running the workflow, the reference data sets QIAseq xHYB Long Read Panels hg19 or QIAseq xHYB Long Read Panels T2T-CHM13v2.0 can now be selected in the "Specify reference data handling" wizard step.

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