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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
  • 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)
• 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
• 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
    • 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

Convert Legacy QIAseq Custom Analyses

Data produced using QIAseq custom panels should be analyzed as described in QIAseq custom panels.

Custom analyses created with the Analyze QIAseq Samples tool in versions 23.x and earlier^12.1 are no longer supported. The QIAseq Panel Analysis Assistant warns about existing legacy custom analyses (figure 12.2). Clicking on Convert starts the Convert Legacy QIAseq Custom Analyses tool. The tool can also be found here:

        Toolbox | Legacy Tools () | Convert Legacy QIAseq Custom Analyses ()

Figure 12.2: The QIAseq Panel Analysis Assistant warns about existing legacy custom analyses.

Convert Legacy QIAseq Custom Analyses helps converting custom analyses by creating custom sets and/or pre-configured workflow copies. Starting the tool opens a wizard listing the identified custom analyses on the left side, and details and available options for the selected custom analysis on the right side (figure 12.3).

Figure 12.3: A custom analysis for Targeted DNA that uses the "QIAseq DNA Panels hg19" Reference Data Set. There are two custom elements that are specific to this custom analysis, but the element used for the target primers could not be located. The custom analysis uses a different genetic code than the default in the template workflows.

The right side of the wizard contains the following:

Reference data set.

• A custom analysis is based on a certain Reference Data Set, which is listed at the top of the wizard.
• All missing Reference Data Elements can be downloaded by clicking on the Download to Workbench button.
• If the CLC Workbench is logged into a CLC Server, there is also a Download to Server button.
• The download buttons are disabled when all Reference Data Elements have been downloaded.

Custom elements.

• A custom analysis usually uses a few custom elements that are different than those in the Reference Data Set. These are listed below the Reference Data Set.
• Navigate to the different custom elements in the Navigation Area by clicking on the () button.
• Custom elements that cannot be located are marked with () and the () button is disabled.
• Create a custom set starting from the Reference Data Set and using the custom elements, by clicking on Create Custom Set.
  • If all needed Reference Data Elements have been previously downloaded to the CLC Workbench, or, if relevant, to the CLC Server that the CLC Workbench is logged into, the "Create Custom Data Set" wizard opens.
  • If there are missing Reference Data Elements, a warning wizard is shown (figure 12.4). Clicking Yes opens the "Create Custom Data Set" wizard and the missing Reference Data Elements are marked with () (figure 12.5).
  • The set can be further customized and saved from the "Create Custom Data Set" wizard (figure 12.5).

Figure 12.4: Creating a Custom Set shows a warning message when there are missing Reference Data Elements.

Figure 12.5: Creating a Custom Set for the custom analysis. Both the genes Reference Data Element and the target primers custom element are missing.

Custom settings.

• Some custom analyses could use a different genetic code than default in the template workflows. If relevant, this is listed below the custom elements.

Workflows.

• A custom analysis is based on an existing panel or kit, for which multiple workflows can be available. All relevant workflows are listed at the bottom of the wizard.
• Navigate to the selected template workflow in the Toolbox by clicking on the Find in Toolbox button.
• Open a workflow copy by clicking on the Open Copy button.
  • The workflow copy is configured with the relevant Reference Data Set, including the custom elements.
  • If all needed Reference Data Elements have been previously downloaded to the CLC Workbench, or, if relevant, to the CLC Server that the CLC Workbench is logged into, the copy opens in the background.
  • If there are missing Reference Data Elements, a "Reference data" wizard offers to download them. The download can be skipped by clicking Finish.
  • When there are missing Reference Data Elements and/or custom elements, the workflow fails to validate. To run the workflow, either download the missing Reference Data Element and/or configure the workflow to use different data.
  • If a different genetic code was used, the workflow is configured accordingly.
  • The workflow can be further customized and once it is saved to the Navigation Area, it can be installed, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Creating_workflow_installation_file for details.

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Footnotes

... earlier^12.1

Versions of the Biomedical Genomics Analysis plugin prior to 24.0 had support for adding custom analyses to the Analyze QIAseq Samples tool. From version 24.0, the Analyze QIAseq Samples tool has been replaced by the QIAseq Panel Analysis Assistant, which does not support custom analyses.

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