Identify QIAseq Somatic Variants (WGS) (Illumina)
Identify QIAseq Somatic Variants (WGS) (Illumina) is designed to call somatic variants from DNA data produced with the library kits QIAseq Multimodal DNA/RNA Library Kit, QIAseq FX DNA Library Kit and QIAseq Ultralow Input Library Kit.
The workflow includes all necessary steps for processing and analyzing the DNA reads:
- Various statistics summarizing and visualizing the input reads are produced using QC for Sequencing Reads, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Sequencing_Reads.html
- Reads are trimmed using Trim Reads, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_Reads.html
- Reads are mapped using Map Reads to Reference, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Map_Reads_Reference.html
- A guidance track is generated from the mapped (UMI) reads using Structural Variant Caller
- An improved mapping is obtained by realigning the mapped (UMI) reads using the guidance track and Local Realignment, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Local_Realignment.html
- Variants are called from the improved mapping using Low Frequency Variant Detection, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Low_Frequency_Variant_Detection.html. For panel data, variant calling is restricted to the relevant target regions.
- The variants are annotated with various information, such as the relation to repeat/homopolymer regions or gene elements, and are subsequently filtered to remove those that are likely to be artifacts through a filtering cascade using Filter on Custom Criteria, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Filter_on_Custom_Criteria.html
- A summary report is created using Create Sample Report, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report.html
Launching the workflow
To run the workflow, go to
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq DNA Workflows (
) | Identify QIAseq Somatic Variants (WGS) (Illumina) (
)
For general information about launching workflows, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Launching_workflows_individually_in_batches.html
Options in the following dialogs can be configured:
- Choose where to run. If you are connected to a CLC Server via the CLC Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
- Select Reads. Select the DNA reads. When analyzing more than one sample at a time, check the Batch checkbox in the lower left corner of the dialog.
- Specify reference data handling. Select the QIAseq Multimodal Library Kit and Hybrid Capture hg38 Reference Data Set, see Reference data management for details.
- Configure batching. If running the workflow in Batch mode, you will be asked to define the batch units. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_workflows_in_batch_mode.html for details.
- Identify candidate variants. The filtering cascade has been tuned using samples of relatively high quality and coverage to provide the best possible sensitivity and precision. Additional filtering may be needed, or filtering values may need to be adjusted, when working with low quality/coverage samples or when seeking a different balance between sensitivity and precision. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Filter_on_Custom_Criteria.html for details on how to adjust the options.
- Result handling. Choose if a workflow result metadata and/or log should be saved.
- Save location for new elements. Choose where to save the data, and press Finish to start the analysis.
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