Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina)
The Identify QIAseq Hybrid Capture DNA Germline Variants (Illumina) template workflow is designed to call germline 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 Germline Variants including Mitochondrial (Illumina) should be used (see Identify QIAseq Hybrid Capture DNA Germline Variants including Mitochondrial (Illumina)).
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 Fixed Ploidy 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 Germline 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 workflow steps and output file structure is similar to what is utilized for the Identify QIAseq Exome Germline Variants workflow, which is described in Identify QIAseq Exome Germline Variants. However, an additional filtering step has been introduced for Indels.
Launching using the QIAseq Panel Analysis Assistant
The workflow is also available in the QIAseq Panel Analysis Assistant under xHYB Human.
Subsections