Product manuals
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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
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
IMSEQ
IMGT
Output from 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
Table for Clonotypes
Alignments for Clonotypes
Sankey plot for Clonotypes
Rarefaction for Clonotypes
CDR3 length for Clonotypes
Segment usage for Clonotypes
Cumulative frequencies for Clonotypes
Clonotype Sample Comparison
Tables for Clonotype Sample Comparison
Sankey plot for Clonotype Sample Comparison
Scatter plot for Clonotype Sample Comparison
Rarefaction for Clonotype Sample Comparison
CDR3 length for Clonotype Sample Comparison
Segment usage for Clonotype Sample Comparison
Jaccard distance heat map for Clonotype Sample Comparison
Oncology score estimation
Calculate TMB Score
Detect MSI Status
Output from Detect MSI Status
Generate MSI Baseline
Calculate HRD Score (beta)
IPA and QCI Interpret Upload
Upload to IPA
Upload using the Ingenuity Knowledge Base
Error handling
QCI Interpret Upload
Prepare QCI Interpret Upload
Upload Prepared QCI Interpret Report
Upload to QCI Interpret
General tools
Annotate RNA Variants
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
Finding differentially methylated regions
Create Methylation Level Heat Map
Predict Methylation Profile
Create Methylation Database
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 Mapping workflow
Detect QIAseq MSI Status
Output of the Detect QIAseq MSI Status workflow
Detect MSI Status with Baseline Creation
Identify QIAseq DNA and QIAseq DNA Pro Variants
Introduction to the Identify QIAseq DNA Variants workflows
Running the Identify QIAseq DNA Variants workflows
Output from the Identify QIAseq DNA Variants workflows
Quality Control for the Identify QIAseq DNA Variants workflow
Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair (Illumina)
Output from the Identify QIAseq DNA Somatic and Germline Variants from Tumor Normal Pair (Illumina) workflow
Identify QIAseq DNA Pro Somatic Variants with LOH Detection
Output from the Calculate LOH workflow
Identify QIAseq DNA Pro Somatic Variants with MSI (Illumina)
Output from the Identify QIAseq DNA Pro Somatic Variants with MSI (Illumina) 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
Output from the Identify QIAseq DNA Ultra Somatic Variants template workflow
Create QIAseq DNA Ultra CNV Control Mapping
Output from the Create QIAseq DNA Ultra CNV Control Mapping template workflow
Create QIAseq Hybrid Capture CNV Control Mapping (Illumina)
Output from the Create QIAseq Hybrid Capture CNV Control Mapping (Illumina)
Identify QIAseq Hybrid Capture Causal Inherited Variants in Trio
Output from the Identify QIAseq Hybrid Capture Causal Inherited Variants in Trio
Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina)
Output from the Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina) workflow
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 Library Kit Variants
Output from the Identify QIAseq Multimodal DNA Library Kit Variants workflows
Create QIAseq Hybrid Capture CNV Control Mapping (with UMI) (Illumina)
Identify QIAseq Somatic Variants (WGS) (Illumina)
Output from the Identify QIAseq Somatic Variants (WGS) (Illumina) template workflow
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 workflows
Perform QIAseq FastSelect RNA Analysis
Output from the Perform QIAseq FastSelect RNA Analysis workflow
Detect Wells for UPXome
Demultiplex QIAseq UPXome Reads
Perform QIAseq UPXome RNA Analysis
Output from the Perform QIAseq UPXome RNA Analysis workflow
Perform QIAseq Multimodal RNA Library Kit Analysis
Output from the Perform QIAseq Multimodal RNA Library 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)
Filter Somatic Variants (WGS)
Identify Somatic Variants from Tumor Normal Pair (WGS)
Identify Variants (WGS)
Hereditary Disease (WGS)
Filter Causal Variants (WGS-HD)
Identify Variants (WGS-HD)
Whole exome sequencing (WES)
General Workflows (WES)
Annotate Variants (WES)
Annotate Variants with Effect Scores (WES)
Identify Known Variants in One Sample (WES)
Somatic Cancer (WES)
Filter Somatic Variants (WES)
Identify Somatic Variants from Tumor Normal Pair (WES)
Identify Variants (WES)
Identify and Annotate Variants (WES)
Hereditary Disease (WES)
Filter Causal Variants (WES-HD)
Identify Variants (WES-HD)
Identify and Annotate Variants (WES-HD)
Targeted amplicon sequencing (TAS)
General Workflows (TAS)
Annotate Variants (TAS)
Identify Known Variants in One Sample (TAS)
Somatic Cancer (TAS)
Filter Somatic Variants (TAS)
Run the Filter Somatic Variants (TAS) workflow
Output from the Filter Somatic Variants (TAS) workflow
Identify Somatic Variants from Tumor Normal Pair (TAS)
Identify Variants (TAS)
Identify and Annotate Variants (TAS)
Hereditary Disease (TAS)
Filter Causal Variants (TAS-HD)
Run the Filter Causal Variants (TAS-HD) workflow
Output from the Filter Causal Variants (TAS-HD) workflow
Identify Variants (TAS-HD)
Identify and Annotate Variants (TAS-HD)
Whole transcriptome sequencing (WTS)
Differential Expression and Pathway Analysis
Output from the Differential Expression and Pathway Analysis workflows
Annotate Variants (WTS)
Compare Variants in DNA and RNA
Identify Candidate Variants and Genes from Tumor Normal Pair
Identify Variants and Add Expression Values
Legacy workflows
QIAGEN GeneRead Panel Analysis (legacy)
Output from QIAGEN GeneRead Panel Analysis (legacy)
Install and uninstall plugins
Installation of plugins
Uninstalling plugins
Bibliography
Oncology score estimation
The oncology score estimation folder contains tools related to TMB, MSI and HRD.
Subsections
Calculate TMB Score
Detect MSI Status
Generate MSI Baseline
Calculate HRD Score (beta)