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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
- Validate QIAseq Read Structure (beta)
  - Output from Validate QIAseq Read Structure (beta)
- 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 Identify QIAseq DNA Ultra Somatic Variants template workflow
- The Calculate LOH template workflow
  - Output from the Calculate LOH workflow
- 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
- 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' RNA
- Demultiplex QIAseq UPX 3' reads
- The Quantify QIAseq UPX 3' template workflow
  - Output from the Quantify QIAseq UPX 3' workflow
FastSelect RNA
- Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer) workflow
- Perform QIAseq FastSelect Rna Expression and Fusion Calling (N6-T RT primer)
  - Output for the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT primer) workflow
UPXome RNA
- Detect Wells
- Running the QIAseq UPXome workflows
- The Demultiplex QIAseq UPXome Reads workflow
- Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT + ODT-RT primer) workflow
- Perform QIAseq UPXome Rna Expression and Fusion Calling (N6-T RT primer)
  - Output for the Perform QIAseq UPXome RNA Expression and Fusion Calling (N6-T RT primer) workflow
Exome and xHYB
- Identify QIAseq Exome Germline Variants
  - Output from the Identify QIAseq Exome Germline Variants template workflow
- Identify QIAseq xHYB Germline Variants
  - Identify QIAseq xHYB Germline Variants including Mitochondrial
- Identify QIAseq xHYB Somatic Variants
  - Identify QIAseq xHYB Somatic Variants including Mitochondrial
- 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
- Structural Variant Caller
  - Output from the Structural Variant Caller
- Detect Regional Ploidy
  - Output from Detect Regional Ploidy
- Calculate HRD Score (beta)
- Target Region Coverage Analysis
  - Output from Target Region Coverage Analysis
Batching workflows
Legacy tools
- CNV and LOH Detection
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

Generate MSI Baseline

The tool Generate MSI Baseline can be used to generate MSI baseline tracks. To do so, go to:

Tools | QIAseq Panel Expert Tools () | QIAseq DNA Panel Expert Tools () | Generate MSI Baseline ()

First you must select at least five read mappings as inputs, but for the most optimal result, we recommend that you use read mappings from at least 15 normal samples.

You can then specify a microsatellite loci track and set up the parameters seen on figure 6.62.

Image generatemsi
Figure 6.62: Parameters for the Generate MSI Baseline tool

You can change the Flanking signature length that is set by default at 8. You can also choose to allow one mismatch in the flanking signature, or none at all when deselecting this option. Finally, you can choose to ignore broken pairs.

Note that all the MSI baseline tracks available in the QIAseq TMB Panels hg38 Reference Data Set have been generated from samples that were mapped against the hg38 (no alternative analysis set) reference sequence.