• Product manuals

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• Introduction
  • The concept of Biomedical Genomics Analysis
  • System requirements
  • Contact information
• Data import and export
  • BGI/MGI Sequencing Import
  • Illumina Custom Reads
• Reference Data Management
  • QIAGEN Sets
• 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
• QIAseq Panel Analysis
  • The Analyze QIAseq Panels guide
    • Import your reads
    • Start a QIAseq panel analysis
    • Upload to QCI Interpret
  • How to create a custom panel analysis workflow
    • Import QIAGEN Primers
  • Create a custom Trim adapter list (optional)
  • Unique Molecular Indexes (UMIs)
    • UMI group sizes
• Targeted DNA
  • The Identify QIAseq DNA Variants ready-to-use 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
  • Create QIAseq DNA CNV Control Mapping workflows
    • Output from the Create QIAseq DNA CNV Control Samples workflow
  • The Identify TMB Status ready-to-use workflows
    • Output from the Identify TMB Status workflow
  • The Detect QIAseq MSI Status ready-to-use workflow
    • Output of the Detect QIAseq MSI Status workflow
  • Detect MSI Status with Baseline Creation ready-to-use workflow
  • Targeted DNA tools detailed description
    • Annotate Structural Variants
    • Convert Annotation Track Coordinates
    • Calculate TMB Score
    • Detect MSI Status
    • Extract Reads Matching Primers
    • Generate MSI Baseline
    • Refine Read Mapping
    • Remove and Annotate with Unique Molecular Index
    • Calculate Unique Molecular Index Groups
    • Create UMI Reads from Grouped Reads
    • Create UMI Reads from Reads
    • Remove Ligation Artifacts
    • Trim Primers of Mapped Reads
    • Identify Mispriming Events
    • Annotate Variants with Unique Molecular Index Info
    • Prepare Guidance Variant Track
    • Import Gene-Pseudogene Table
• Targeted RNAscan
  • The Detect QIAseq RNAscan Fusions ready-to-use workflow
    • Output from the Detect QIAseq RNAscan Fusions workflow
  • The Perform QIAseq RNA Fusion XP Analysis ready-to-use workflows
    • Output from the Perform QIAseq RNA Fusion XP Analysis workflow
  • Interpretation of fusion results
  • Targeted RNAscan tools detailed description
    • Detect and Refine Fusion Genes
    • Annotate Fusions with Known Fusion Information
    • QC for RNAscan Panels
    • Annotate RNA Variants
    • Import Known Fusion Information Track
• Immune Repertoire
  • Perform QIAseq Immune Repertoire Analysis ready-to-use workflow
    • Output from the Perform QIAseq Immune Repertoire Analysis workflow
  • QIAseq Immune Repertoire Expert Tools
    • Import VDJtools Clonotypes
    • Immune Repertoire Analysis
    • Compare Immune Repertoires
• Targeted Multimodal
  • Perform QIAseq Multimodal Analysis (Illumina) ready-to-use workflow
    • Output from the Perform QIAseq Multimodal Analysis (Illumina)
  • Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina) ready-to-use workflow
    • Output from the Perform QIAseq Multimodal Analysis with TMB and MSI (Illumina)
  • Running the workflows in batch using Metadata
• Targeted RNA
  • The Quantify QIAseq RNA Expression ready-to-use workflow
    • Output from the Quantify QIAseq RNA Expression workflow
  • Targeted RNA tools detailed description
    • The Quantify QIAseq RNA tool
• UPX 3'
  • Demultiplex QIAseq UPX 3' reads
  • The Quantify QIAseq UPX 3' ready-to-use workflow
    • Output from the Quantify QIAseq UPX 3' workflow
• Exome
  • Identify QIAseq Exome Germline Variants
    • Output from the Identify QIAseq Exome Germline Variants ready-to-use workflow
  • 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 ready-to-use workflow
• Targeted Methyl
  • The Detect QIAseq Methylation ready-to-use workflow
    • Output from the Detect QIAseq Methylation workflow
  • Targeted Methyl associated tools
    • Finding differentially methylated regions
    • Create Methylation Level Heat Map
• QCI Interpret Integration
  • Upload to QCI Interpret
  • Prepare QCI Interpret Upload
  • Upload Prepared QCI Interpret Report
• QIAseq miRNA Analysis
  • QIAseq miRNA Quantification
    • QIAseq miRNA Quantification outputs
    • Naming isomiRs
  • QIAseq miRNA Differential Expression
  • QIAseq miRNA Expert Tools
    • Create UMI Reads for miRNA
• TruSight Oncology 500
  • The Perform TSO500 DNA Analysis (Illumina) workflow
    • Output from the Perform TSO500 DNA Analysis
  • The Perform TSO500 RNA Analysis (Illumina) workflow
    • Output from the Perform TSO500 RNA Analysis
• QIAGEN GeneRead DNA Panel Analysis
  • The QIAGEN GeneRead Panel Analysis workflow
    • Output from the QIAGEN GeneRead Panel Analysis
  • Trim Primers and their Dimers from Mapping
• Ready-to-use workflows descriptions and guidelines
  • General Workflow
  • Somatic Cancer
  • Hereditary Disease
• Getting started
  • Import sequencing data
  • Prepare Raw Data
• 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 Causal Inherited Variants in Family of Four (WGS)
    • Identify Causal Inherited Variants in Trio (WGS)
    • Identify Rare Disease Causing Mutations in Family of Four (WGS)
    • Identify Rare Disease Causing Mutations in Trio (WGS)
    • 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 Causal Inherited Variants in Family of Four (WES)
    • Identify Causal Inherited Variants in Trio (WES)
    • Identify Rare Disease Causing Mutations in Family of Four (WES)
    • Identify Rare Disease Causing Mutations in Trio (WES)
    • 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)
    • Identify Somatic Variants from Tumor Normal Pair (TAS)
    • Identify Variants (TAS)
    • Identify and Annotate Variants (TAS)
  • Hereditary Disease (TAS)
    • Filter Causal Variants (TAS-HD)
    • Identify Causal Inherited Variants in Family of Four (TAS)
    • Identify Causal Inherited Variants in Trio (TAS)
    • Identify Rare Disease Causing Mutations in Family of Four (TAS)
    • Identify Rare Disease Causing Mutations in Trio (TAS)
    • Identify Variants (TAS-HD)
    • Identify and Annotate Variants (TAS-HD)
• 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
• General tools
  • Create Consensus Sequences from Variants
  • CNV and LOH Detection
    • Region-level CNV track (Region CNVs)
    • Target-level CNV track (Target CNVs)
    • Gene-level annotation track (Gene CNVs)
    • Loss-of-heterozygosity track
    • CNV results report
    • CNV algorithm report
  • Structural Variant Caller
    • Output from the Structural Variant Caller
  • Target Region Coverage Analysis
    • Output from Target Region Coverage Analysis
• Batching workflows
• Legacy tools
  • Detect Fusion Genes
  • Refine Fusion Genes
• Appendices
  • Install and uninstall plugins
    • Installation of plugins
    • Uninstalling plugins
• Bibliography

Data import and export

Most import and export of data is done using the tools delivered as part of the CLC Genomics Workbench. This functionality is described at https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Import_export_data_graphics.html.

This chapter describes only import/export functionality specific to the Biomedical Genomics Analysis.

Data import

Data import is generally done using the standard tools of the CLC Genomics Workbench. This includes the on-the-fly import functionality available when launching workflows, described at:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Importing_data_on_fly.html.

Direct access to certain NGS importers is also provided via the Analyze QIAseq Panels tool, as described in this section.

Reference data import is described in Reference Data Management.

Data export

General data export documentation is available at https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Data_export.html.

Note that VCF format files can be uploaded directly to QCI Interpret, or the Upload to QCII tool can be used to upload data from CLC Genomics Workbench without explicitly exporting it first. Use of Upload to QCII is described in QCI Interpret Integration.

SAM/BAM export of UMI read mappings When exporting UMI reads to SAM or BAM format, a UMI will be described as Unique_Molecular_Index=[number1]_count=[number2]. Here number1 is a UMI ID (just a unique UMI group number), and number2 is the number of reads that are in that UMI group.

This information is relevant to the export of relevant outputs from workflows distributed with this plugin for analyzing data generated using some types of QIAseq panels, such as:

• Targeted DNA Panels
• Targeted RNAscan Panels
• UPX 3' RNA Panels
• Multimodal Panels
• RNA Fusion XP

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Subsections

• BGI/MGI Sequencing Import
• Illumina Custom Reads

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