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) (
)
Running the workflow, and the outputs generated, is similar to the Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina) workflow, which is described in detail in Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina). However, the Low Frequency Variant Detection tool is used for variant detection instead of the Fixed Ploidy Variant Detection tool and a different filtering step has been introduced as outlined below:
- Low Frequency Variant Detection. Configure the variant detection options. For additional details, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Low_Frequency_Variant_Detection.html.
- Remove Marginal Variants. Set the minimum frequency for detected variants.
Launching using the QIAseq Panel Analysis Assistant
The workflow is also available in the QIAseq Panel Analysis Assistant under Human Exome.
Subsections