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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
Template Workflows
Subsections
General Template Workflows
Template Workflows - QIAseq Targeted DNA
Template Workflows - QIAseq Targeted DNA Pro