Identify QIAseq Hybrid Capture DNA Somatic Variants (Illumina)
The Identify QIAseq Hybrid Capture DNA Somatic Variants (Illumina) template workflow is designed to call somatic variants from data generated with e.g. QIAseq Multimodal DNA Library kit without UMIs or QIAseq FX DNA Library kit followed by hybrid capture-based target enrichment without addition of mitochondrial spike-in probes, such as QIAseq Exome, QIAseq xHYB Human, or panels from a third party provider. For panels from a third party provider, the same approach as described in QIAseq custom panels is recommended.
If mitochondrial spike-in probes have been added, the Identify QIAseq Hybrid Capture DNA Somatic Variants including Mitochondrial (Illumina) should be used (see Identify QIAseq Hybrid Capture DNA Somatic Variants including Mitochondrial (Illumina)).
For data generated using QIAseq Multimodal DNA Library kit with UMIs, see Identify QIAseq Multimodal DNA Lib Kit and Hybrid Capture Variants.
The first steps of the workflow involve trimming off any remaining PCR adapters. This is followed by mapping the trimmed reads to the human reference sequence. The Structural Variant Caller then generates a guidance track that is used in the Local Realignment tool to improve the mapping. The improved mapping is then input to the Low Frequency Variant Detection tool. The resulting variants are filtered to remove those located outside defined target regions. Remaining variants are then annotated with information such as the relation to repeat/homopolymer regions or gene elements. Finally, a series of filtering steps removes variants likely to be artifacts. The retained variants are output, along with reports and other associated results.
The workflow can be found at:
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq DNA workflows (
) | Identify QIAseq Hybrid Capture DNA Somatic Variants (Illumina) (
)
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.
The initial steps of the workflow for selecting reads and the appropriate reference data, as well as mapping reads to the reference, are similar to the Identify QIAseq Exome Germline Variants workflow, which is described in Identify QIAseq Exome Germline Variants.
For variant detection, the Low Frequency Variant Detection tool is used. The parameters for this tool can be set in the relevant wizard step when launching the workflow (figure 13.58). For a description of the different parameters that can be adjusted, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Low_Frequency_Variant_Detection.html. If you click on "Locked Settings", you will be able to see all parameters used for variant detection in the template workflow (figure 13.58).
Figure 13.58: Specify the parameters for the Low Frequency Variant Detection tool.
The Copy Number Variant Detection tool is used for detection of copy number variants when control mappings are provided, as described for the Identify QIAseq Exome Germline Variants workflow in Identify QIAseq Exome Germline Variants. Mapping of control samples can be performed using the workflow described in Create QIAseq Exome CNV Control Mapping and specifying the relevant target regions in the Target regions wizard step.
The settings of a comprehensive variant filtering cascade can be adjusted in a series of wizard steps.
In the final wizard step, choose to Save the results of the workflow and specify a location in the Navigation Area before clicking Finish.
Launching using the QIAseq Panel Analysis Assistant
The workflow is also available in the QIAseq Panel Analysis Assistant under xHYB Human.
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