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Introduction
The concept of Biomedical Genomics Analysis
System requirements
Contact information
Getting started
Data import and export
Import sequencing data
Prepare raw data
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
Create UMI Reads from Reads
Create UMI Reads for miRNA
Annotate Variants with Unique Molecular Index Info
QIAseq tools
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
IMSEQ
IMGT
Output from Import Immune Reference Segments
Immune Repertoire Analysis
Output from the Immune Repertoire Analysis tool
Filter Immune Repertoire
Compare Immune Repertoires
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)
QCI Interpret integration
Prepare QCI Interpret Upload
Upload Prepared QCI Interpret Report
Upload to QCI Interpret
Haplotype Calling (beta)
Genotype track
Genome model
Locus table
Allele table
Header view
Track view
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
Finding differentially methylated regions
Create Methylation Level Heat Map
Predict Methylation Profile
Create Methylation Database
Trim Primers and their Dimers from Mapping
Batching workflows
QIAseq sample analysis
The Analyze QIAseq Samples guide
Import your reads
Start a QIAseq sample analysis
Guide Upload to QCI Interpret
How to create a custom sample analysis workflow
Import QIAGEN Primers
Create a custom Trim adapter list (optional)
UMI group sizes
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
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 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
Exome and xHYB template workflows
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 xHYB Germline Variants
Identify QIAseq xHYB Germline Variants including Mitochondrial
Identify QIAseq xHYB Somatic Variants
Identify QIAseq xHYB Somatic Variants including Mitochondrial
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
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
Reference data sets for immune workflows
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 Analysis
Output from the Perform QIAseq Multimodal Analysis (Illumina)
Running multimodal workflows in batch using metadata
Perform QIAseq Multimodal Analysis with TMB and MSI
Output from the Perform QIAseq Multimodal 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)
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
Install and uninstall plugins
Biomedical Genomics Analysis is installed as a plugin.
Subsections
Installation of plugins
Uninstalling plugins