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Introduction
- The concept of Biomedical Genomics Analysis
- System requirements
- Contact information
Data import and export
Reference Data Management
- QIAGEN Sets
SARS-CoV-2 workflows
- Identify ARTIC V3 SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
- Identify QIAseq SARS-CoV-2 Low Frequency and Shared Variants (Illumina)
- Identify Ion AmpliSeq SARS-CoV-2 Low Frequency and Shared Variants (Ion Torrent)
- SARS-CoV-2 workflow output
  - Summary outputs
  - Sample specific outputs
QIAseq Sample Analysis
- The Analyze QIAseq Samples guide
- How to create a custom sample analysis workflow
  - Import QIAGEN Primers
- Create a custom Trim adapter list (optional)
- Unique Molecular Indexes (UMIs)
  - UMI group sizes
Targeted DNA
- The Identify QIAseq DNA Variants template workflows
- Create QIAseq DNA CNV Control Mapping workflows
  - Output from the Create QIAseq DNA CNV Control Samples workflow
- The Identify TMB Status template workflows
  - Output from the Identify TMB Status workflow
- The Detect QIAseq MSI Status template workflow
  - Output of the Detect QIAseq MSI Status workflow
- Detect MSI Status with Baseline Creation template workflow
- The Perform QIAseq cfDNA Analysis template workflow
  - Output from the Perform QIAseq cfDNA analysis workflow
- The Identify HRD Score template workflows
  - Output from the Identify HRD Score workflows
- Targeted DNA tools detailed description
Targeted RNAscan
- The Detect QIAseq RNAscan Fusions template workflow
  - Output from the Detect QIAseq RNAscan Fusions workflow
- The Perform QIAseq RNA Fusion XP Analysis template workflows
  - Output from the Perform QIAseq RNA Fusion XP Analysis workflow
- Interpretation of fusion results
- Targeted RNAscan tools detailed description
Immune Repertoire
- Perform QIAseq Immune Repertoire Analysis template workflow
  - Output from the Perform QIAseq Immune Repertoire Analysis workflow
- QIAseq Immune Repertoire Expert Tools
Targeted Multimodal
- Perform QIAseq Multimodal Analysis (Illumina) template workflow
  - Output from the Perform QIAseq Multimodal Analysis (Illumina)
- Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) template workflow
  - Output from the Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)
- Running the workflows in batch using Metadata
Targeted RNA
- The Quantify QIAseq RNA Expression template workflow
  - Output from the Quantify QIAseq RNA Expression workflow
- Targeted RNA tools detailed description
  - The Quantify QIAseq RNA tool
UPX 3'
- Demultiplex QIAseq UPX 3' reads
- The Quantify QIAseq UPX 3' template workflow
  - Output from the Quantify QIAseq UPX 3' workflow
UPXome
- Detect Wells
- The Quantify QIAseq UPXome template workflow
  - Output from the Quantify QIAseq UPXome workflow
Exome
- Identify QIAseq Exome Germline Variants
  - Output from the Identify QIAseq Exome Germline Variants template workflow
- Create QIAseq Exome CNV Control Mapping
  - Output from the Create QIAseq Exome CNV Control Mapping workflow
- Identify QIAseq Exome Causal Inherited Variants in Trio
  - Output from the Identify QIAseq Exome Causal Inherited Variants in Trio template workflow
Targeted Methyl
- The Detect QIAseq Methylation template workflows
  - Output from the Detect QIAseq Methylation workflow
- Targeted Methyl associated tools
QCI Interpret Integration
- Upload to QCI Interpret
- Prepare QCI Interpret Upload
- Upload Prepared QCI Interpret Report
QIAseq miRNA Analysis
- QIAseq miRNA Quantification
  - QIAseq miRNA Quantification outputs
  - Naming isomiRs
- QIAseq miRNA Differential Expression
- QIAseq miRNA Expert Tools
  - Create UMI Reads for miRNA
TruSight Oncology 500
- The Perform TSO500 DNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 DNA Analysis
- The Perform TSO500 RNA Analysis (Illumina) workflow
  - Output from the Perform TSO500 RNA Analysis
QIAGEN GeneRead DNA Panel Analysis
- The QIAGEN GeneRead Panel Analysis workflow
  - Output from the QIAGEN GeneRead Panel Analysis
- Trim Primers and their Dimers from Mapping
Template workflows descriptions and guidelines
- General Workflow
- Somatic Cancer
- Hereditary Disease
Getting started
- Import sequencing data
- Prepare Raw Data
Whole genome sequencing (WGS)
- General Workflows (WGS)
  - Annotate Variants (WGS)
  - Identify Known Variants in One Sample (WGS)
- Somatic Cancer (WGS)
- Hereditary Disease (WGS)
  - Filter Causal Variants (WGS-HD)
  - Identify Variants (WGS-HD)
Whole exome sequencing (WES)
- General Workflows (WES)
- Somatic Cancer (WES)
- Hereditary Disease (WES)
Targeted amplicon sequencing (TAS)
- General Workflows (TAS)
  - Annotate Variants (TAS)
  - Identify Known Variants in One Sample (TAS)
- Somatic Cancer (TAS)
- Hereditary Disease (TAS)
Whole Transcriptome Sequencing (WTS)
- Annotate Variants (WTS)
- Compare Variants in DNA and RNA
- Identify Candidate Variants and Genes from Tumor Normal Pair
- Identify Variants and Add Expression Values
- Identify and Annotate Differentially Expressed Genes and Pathways
General tools
- Create Consensus Sequences from Variants
- CNV and LOH Detection
- Structural Variant Caller
  - Output from the Structural Variant Caller
- Target Region Coverage Analysis
  - Output from Target Region Coverage Analysis
Batching workflows
Legacy workflows
- Identify Causal Inherited Variants in Family of Four (WGS)
- Identify Causal Inherited Variants in Trio (WGS)
- Identify Rare Disease Causing Mutations in Family of Four (WGS)
- Identify Rare Disease Causing Mutations in Trio (WGS)
- Identify Causal Inherited Variants in Family of Four (WES)
- Identify Causal Inherited Variants in Trio (WES)
- Identify Rare Disease Causing Mutations in Family of Four (WES)
- Identify Rare Disease Causing Mutations in Trio (WES)
- Identify Causal Inherited Variants in Family of Four (TAS)
- Identify Causal Inherited Variants in Trio (TAS)
- Identify Rare Disease Causing Mutations in Family of Four (TAS)
- Identify Rare Disease Causing Mutations in Trio (TAS)
Appendices
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

The Identify HRD Score template workflows

Three workflows have been set up to report an HRD score:

Identify QIAseq DNA Somatic Variants with HRD Score (Illumina) (beta)
Identify QIAseq DNA Somatic Variants with HRD Score (Ion Torrent) (beta)
Identify QIAseq DNA Somatic and Germline Variants with HRD Score from Tumor Normal Pair (Illumina) (beta)

The two Identify QIAseq DNA Somatic Variants with HRD Score workflows are built on Identify QIAseq DNA somatic variants. Compared to the original workflow only a few changes have been made. The Calculate LOH and HRD tool with relevant inputs has been included, the parameter defining graining level in the Copy Number Variant Detection (CNVs) tool has been set to fine and an input to Control mappings in the Copy Number Variant Detection (CNVs) is now mandatory.

The workflow Identify QIAseq DNA Somatic and Germline Variants with HRD Score from Tumor Normal Pair is built on Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair. Compared to the original workflow, the Calculate LOH and HRD and Copy Number Variant Detection (CNVs) tools with relevant inputs have been included.

In all three HRD workflows, an additional variant output listing variants in target regions overlapping 15 Homologue Recombination Repair genes is also included to facilitate easy inspection of variants in these genes.

Note that the Calculate LOH and HRD (beta) tool takes a target region track produced by a CNV detection tool as input. Therefore, to run this workflow, control mappings for the CNV baseline must be available. Control mappings can be generated with the workflow Create QIAseq DNA CNV Control Mapping (Illumina/Ion Torrent), see section Create QIAseq DNA CNV Control Mapping workflows.

To see a general description of the workflows and how to start them, go to the manual page for the Identify QIAseq DNA Variants template workflows (The Identify QIAseq DNA Variants template workflows).

The reference data for the QIAseq HRD panel is available in the reference data set QIAseq RNA panels hg19.

Subsections

Output from the Identify HRD Score workflows