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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

Bibliography

Amemiya et al., 2019

Amemiya, H. M., Kundaje, A., and Boyle, A. P. (2019).
The encode blacklist: identification of problematic regions of the genome.
Scientific reports, 9(1):1-5.

Vega et al., 2021

Vega, D., Yee, L., McShane, L., Williams, P., Chen, L., Vilimas, T., Fabrizio, D., Funari, V., Newberg, J., Bruce, L., Chen, S.-J., Baden, J., Barrett, J. C., Beer, P., Butler, M., Cheng, J.-H., Conroy, J., Cyanam, D., Eyring, K., Garcia, E., Green, G., Gregersen, V., Hellmann, M., Keefer, L., Lasiter, L., Lazar, A., Li, M.-C., MacConaill, L., Meier, K., Mellert, H., Pabla, S., Pallavajjalla, A., Pestano, G., Salgado, R., Samara, R., Sokol, E., Stafford, P., Budczies, J., Stenzinger, A., Tom, W., Valkenburg, K., Wang, X., Weigman, V., Xie, M., Xie, Q., Zehir, A., Zhao, C., Zhao, Y., Stewart, M., and on behalf of the TMB Consortium, J. A. (2021).
Aligning tumor mutational burden (tmb) quantification across diagnostic platforms: phase ii of the friends of cancer research tmb harmonization project.
Annals of Oncology, 132(12):1626-1636.

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