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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
    • 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
    • Calculate TMB Score (LightSpeed)
    • Copy Number Variant Detection (WGS)
      • Copy Number Variant Detection (WGS) outputs
• 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
• Bibliography

Compatibility with CLC Genomics Workbench tools

Read mappings produced by the tools LightSpeed Fastq to Germline Variants, LightSpeed Fastq to Somatic Variants and LightSpeed Fastq to Somatic Variants Tumor Normal differ in some fundamental ways from read mappings produced by the Map Reads to Reference tool, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Map_Reads_Reference.html. The main differences are related to how base quality scores and unaligned ends are handled:

• Base quality scores The Lightspeed tools access and use the base quality scores during variant calling, but for efficiency reasons the base quality scores on the individual bases are not kept and stored on individual bases in the final read mapping. CLC Genomics Workbench tools that rely on quality scores being available on bases in a read mapping (such as the variant callers Fixed Ploidy Variant Detection, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Fixed_Ploidy_Variant_Detection.html and Low Frequency Variant Detection, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Low_Frequency_Variant_Detection.html) cannot be expected to perform as well on a read mapping produced by a Lightspeed tool as on a read mapping produced with the Map Reads to Reference tool available in CLC Genomics Workbench.
• Unaligned ends The Lightspeed tools include a structural variant detection step and a subsequent realignment step. In the structural variant detection step, structural variants are inferred from unaligned ends, and the realignment step uses the inferred structural variants during realignment. The realignment procedure differs from that used by the Local Realignment tool, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Local_Realignment.html (available in CLC Genomics Workbench) in that unaligned ends that equally well support different alleles are kept unaligned. CLC Genomics Workbench tools that rely on unaligned ends in a read mapping (such as the InDels and Structural Variants tool, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=InDels_Structural_Variants.html) will therefore behave differently on a read mapping produced with Lightspeed tools compared to a read mapping produced with the Map Reads to Reference tool.

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