Browse the manual

Introduction
- The concept of Biomedical Genomics Analysis
- System requirements
- Contact information
Getting started
Reference data management
- QIAGEN Sets
UMI tools
- Remove and Annotate with Unique Molecular Index
- Calculate Unique Molecular Index Groups
- Create UMI Reads from Grouped Reads
  - Consensus nucleotide calculation
- Create UMI Reads from Reads
- Create UMI Reads for miRNA
- UMI group sizes
- Annotate Variants with Unique Molecular Index Info
QIAseq tools
- Import QIAGEN Primers
- Quantify QIAseq RNA
- QC for RNAscan Panels
- Annotate Fusions with Known Fusion Information
- Validate QIAseq Read Structure (beta)
  - Output from Validate QIAseq Read Structure (beta)
Biomedical utility tools
- Annotate Structural Variants
- Extract Reads Matching Primers
- Identify Mispriming Events
  - Output from Identify Mispriming Events
- Remove Ligation Artifacts
- Trim Primers of Mapped Reads
- Convert Annotation Track Coordinates
Immune repertoire analysis
- Import/Export VDJtools Clonotypes
- Import Immune Reference Segments
- Immune Repertoire Analysis
  - Output from the Immune Repertoire Analysis tool
- Merge Immune Repertoire
  - Merging of clonotypes
  - Output from the Merge Immune Repertoire tool
- Filter Immune Repertoire
- Compare Immune Repertoires
  - Resolving of clonotypes
  - Output from Compare Immune Repertoires tool
- Clonotypes
- Clonotype Sample Comparison
Oncology score estimation
- Calculate TMB Score
- Detect MSI Status
  - Output from Detect MSI Status
- Generate MSI Baseline
- Calculate HRD Score (beta)
QCI Interpret integration
- Prepare QCI Interpret Upload
- Upload Prepared QCI Interpret Report
- Upload to QCI Interpret
Haplotype Calling (beta)
- Genotype track
- Microhaplotype Caller (beta)
  - Output from Microhaplotype Caller (beta)
- Convert to Genotype Track (beta)
- Import VCF to Genotype Track (beta)
- Export Genotype VCF (beta)
- Export Genotype CSV (beta)
- Export Marker Genotypes (beta)
General tools
- Annotate RNA Variants
  - Import Known Fusion Information Track
- Detect Regional Ploidy
  - Output from Detect Regional Ploidy
- Import Gene-Pseudogene Table
- Prepare Guidance Variant Track
- Refine Read Mapping
- Structural Variant Caller
  - Output from the Structural Variant Caller
- Targeted Methyl associated tools
- Trim Primers and their Dimers from Mapping
QIAseq Panel Analysis Assistant
- QIAseq custom panels
- Convert Legacy QIAseq Custom Analyses
QIAseq DNA workflows
- Create QIAseq DNA CNV Control Mapping
  - Output from the Create QIAseq DNA CNV Control Samples workflow
- Detect QIAseq MSI Status
  - Output of the Detect QIAseq MSI Status workflow
- Detect MSI Status with Baseline Creation
- Identify QIAseq DNA Variants
- Identify QIAseq DNA Pro Somatic Variants with LOH Detection
  - Output from the Calculate LOH workflow
- Identify QIAseq DNA Somatic Variants with HRD Score (beta)
  - Output from the Identify HRD Score workflow
- Identify QIAseq DNA Somatic Variants with TMB Score
  - Output from the Identify TMB Status workflow
- Identify QIAseq DNA Ultra Somatic Variants
- 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
- Identify QIAseq Exome Germline Variants
  - Output from the Identify QIAseq Exome Germline Variants template workflow
- Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina)
  - Identify QIAseq Hybrid Capture DNA Germline Variants including Mitochondrial (Illumina)
- Identify QIAseq Hybrid Capture DNA Somatic Variants (Illumina)
  - Identify QIAseq Hybrid Capture DNA Somatic Variants including Mitochondrial (Illumina)
- Identify QIAseq Multimodal DNA Lib Kit Variants
  - Output from the Identify QIAseq Multimodal DNA Lib Kit Variants workflows
QIAseq RNA workflows
- Detect QIAseq RNAscan Fusions
  - Output from the Detect QIAseq RNAscan Fusions workflow
- Perform QIAseq RNA Fusion XP Analysis
  - Output from the Perform QIAseq RNA Fusion XP Analysis 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
- Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) workflow
- Detect Wells for UPXome
- Demultiplex QIAseq UPXome Reads
  - Running the QIAseq UPXome workflows
- 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
- Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer)
  - Output from the Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) workflow
- Perform QIAseq Multimodal RNA Lib Kit Analysis
  - Output from the Perform QIAseq Multimodal RNA Lib Kit Analysis workflows
- QIAseq miRNA Differential Expression
- QIAseq miRNA Quantification
  - QIAseq miRNA Quantification outputs
- Quantify QIAseq RNA Expression
  - Output from the Quantify QIAseq RNA Expression workflow
- Demultiplex QIAseq UPX 3' Reads
- Quantify QIAseq UPX 3'
  - Output from the Quantify QIAseq UPX 3' workflow
Other QIAseq workflows
- Detect QIAseq Methylation
  - Output from the Detect QIAseq Methylation workflow
- Perform QIAseq Immune Repertoire Analysis
  - Output from the Perform QIAseq Immune Repertoire Analysis workflow
- Perform QIAseq Targeted TCR Analysis
  - Output from the Perform QIAseq Targeted TCR Analysis workflow
- Perform QIAseq Multimodal Panel Analysis
  - Output from the Perform QIAseq Multimodal Panel Analysis (Illumina)
  - Running multimodal workflows in batch using metadata
- Perform QIAseq Multimodal Panel Analysis with TMB and MSI
  - Output from the Perform QIAseq Multimodal Panel Analysis with TMB and MSI (Illumina)
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
TruSight Oncology 500
- Perform TSO500 DNA Analysis
  - Output from Perform TSO500 DNA Analysis
- Perform TSO500 RNA Analysis
  - Output from Perform TSO500 RNA Analysis
WGS, WES, TAS and WTS template workflow descriptions
- General workflows
- Somatic cancer
- Hereditary disease
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)
- QIAGEN GeneRead Panel Analysis
  - Output from the QIAGEN GeneRead Panel Analysis
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
Appendices
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

Output from the Merge Immune Repertoire tool

Merge Immune Repertoire produces a TCR clonotypes () or BCR clonotypes () element, containing the merged clonotypes.

The tool optionally outputs a report () containing a summary of the performed merging, followed by statistics of the merged clonotypes, see Output from the Immune Repertoire Analysis for details.

The merging summary shows how many clonotypes were merged and the reason for merging:

Similar CDR3. Clonotypes were merged according to Merge clonotypes with similar CDR3.
Without C segment. Clonotypes were merged according to Merge clonotypes without C segment.
Similar CDR3 and without C segment. Clonotypes were merged according to both Merge clonotypes with similar CDR3 and Merge clonotypes without C segment.
Identical. Clonotypes had the same identified segments and the same CDR3 nucleotide sequence.
The Immune Repertoire Analysis tool (Immune Repertoire Analysis) reports such clonotypes as only one clonotype. However, multiple but identical clonotypes can possibly be present in imported clonotypes (see Import/Export VDJtools Clonotypes). Identical clonotypes are always merged by the tool, regardless of the chosen options.
Identical due to preceding merging. Two originally different clonotypes became identical due to preceding merging steps. See Merging of clonotypes for details.
Multiple merge events. The same clonotype might be merged into several clonotypes for different reasons. For example, if a clonotype is merged into two different clonotypes because of similar CDR3, this clonotype will count towards Similar CDR3. If another clonotype is merged into two different clonotypes, one because of similar CDR3 and the other because of missing C, this clonotype will count towards both Similar CDR3, Without C segment and Multiple merge events.