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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
  - Output from Quantify QIAseq RNA
- QC for RNAscan Panels
- Import Known Fusion Information Track
- 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
  - Output from Calculate HRD Score
  - HRD calculation
IPA and QCI Interpret Upload
- Upload to IPA
  - Upload using the Ingenuity Knowledge Base
  - Error handling
- QCI Interpret Upload
General tools
- Annotate RNA Variants
- Detect Regional Ploidy
  - Output from Detect Regional Ploidy
  - Ploidy state detection
- 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
QIAseq DNA workflows
- Analyze QIAseq DNA and QIAseq DNA Pro
  - Output from Analyze QIAseq DNA
  - Quality Control for Analyze QIAseq DNA
- Analyze QIAseq DNA Ultra Somatic
  - Output from Analyze QIAseq DNA Ultra Somatic
- Analyze QIAseq Hybrid Capture DNA
  - Output from Analyze QIAseq Hybrid Capture DNA
- Analyze QIAseq Hybrid Capture DNA Somatic (with UMI)
  - Output from Analyze QIAseq Hybrid Capture DNA Somatic (with UMI)
  - Compare ID SNP variants across samples
- Analyze QIAseq Hybrid Capture DNA in Trio
  - Output from Analyze QIAseq Hybrid Capture DNA in Trio
- Analyze QIAseq Multimodal DNA Panel
  - Output from Analyze QIAseq Multimodal DNA Panel
- Analyze QIAseq Somatic WGS
  - Output from Analyze QIAseq Somatic WGS
- Analyze QIAseq Multimodal DNA Library Kit Somatic WGS (with UMI)
  - Output from Analyze QIAseq Multimodal DNA Library Kit Somatic WGS (with UMI)
- Simplifying filter cascades
QIAseq RNA workflows
- Analyze QIAseq Multimodal RNA Panel
  - Output from Analyze QIAseq Multimodal RNA Panel
- Analyze QIAseq RNA
  - Output from Analyze QIAseq RNA
- Analyze QIAseq RNAscan
  - Output from Analyze QIAseq RNAscan
- Analyze QIAseq RNA Fusion XP
  - Output from Analyze QIAseq RNA Fusion XP
- Demultiplex QIAseq UPX 3' Reads
- Analyze QIAseq UPX 3' RNA
  - Output from Analyze QIAseq UPX 3' RNA
- Analyze QIAseq Multimodal RNA Library Kit
  - Output from Analyze QIAseq Multimodal RNA Library Kit
- Analyze QIAseq FastSelect and UPXome RNA
  - Output from Analyze QIAseq FastSelect and UPXome RNA
  - Detect Wells for UPXome
- Analyze QIAseq miRNA
  - Output from Analyze QIAseq miRNA
Other QIAseq workflows
- Analyze QIAseq Methyl
  - Output from Analyze QIAseq Methyl
- Analyze QIAseq Immune Repertoire
  - Output from the Analyze QIAseq Immune Repertoire (Illumina) workflow
- Analyze QIAseq Targeted TCR
  - Output from the Analyze QIAseq Targeted TCR (Illumina) workflow
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)
  - Filter Somatic Variants (WGS)
  - Identify Variants (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 Variants and Add Expression Values
Comparative analysis
- Analyze Tumor Normal Pair
  - Output from the Analyze Tumor Normal Pair workflow
- Differential Expression Analysis
  - Output from the Differential Expression Analysis workflows
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
Appendix
- QIAseq template workflows consolidation overview
- Install and uninstall plugins
  - Installation of plugins
  - Uninstalling plugins
Bibliography

QCI Interpret Upload

QCI Interpret uses the QIAGEN Knowledge Base - a database that contains over 5 million variant findings as well as data from third party databases - and rules-based approaches to automatically compute pathogenicity classifications (Pathogenic to Benign) and actionability classifications (Tier 1 to 4) for each found variant. Pathogenicity and actionability classifications in QCI Interpret are accompanied by clear visibility into the criteria and evidence supporting the classifications. The final report is sample-specific and includes clinically-relevant variants, interpretations, approved or investigational therapies, and references specified throughout the assessment process.

The Upload to QCI Interpret tools support seamless upload of analysis results to QCI Interpret.

It is possible to upload all variants that can be exported to VCF from the CLC Workbench, as well as TMB and MSI scores. In addition, it is possible to upload CLC reports, which can then be accessed as PDFs in the QCI Interpret platform.

To upload data to QCI Interpret using Upload to QCI Interpret and Upload Prepared QCI Interpret Report you need an active API-enabled QCI Interpret or QCI Interpret Translational account. Please send an email to bioinformaticslicense@qiagen.com and ask for confirmation if the QCI account is API-enabled, for questions about licenses, or to purchase a new license.

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