The first steps in the QIAseq Targeted DNA Panel Analysis template workflows involve trimming remaining PCR adapters, the UMI and the common sequence prefix while retaining the UMI barcoding information as an annotation on the read. This is followed by mapping the trimmed reads to the human reference sequence. After mapping, the Create UMI Reads from Grouped Reads tool generates a single consensus read, called a "UMI read", from reads with the same UMI.
The workflow then removes ligation artifacts from the read mapping. Next, the Indels and Structural Variants detection step generates a guidance track used for improving the mapping with the Local Realignment tool. Variants are then detected on the UMI reads using the Low Frequency Variant Detection tool for somatic workflows, and the Fixed Ploidy Variant Detection tool for germline applications. Finally, a series of filtering steps removes variants likely to be artifacts. The final output of the workflow includes, among other items, a list of filtered variants, including some present at very low frequency in the original dataset.
- Create QIAseq DNA CNV Control Mapping
- Detect QIAseq MSI Status
- Detect MSI Status with Baseline Creation
- Identify QIAseq DNA Variants
- Identify QIAseq DNA Pro Somatic Variants with LOH Detection
- Identify QIAseq DNA Somatic Variants with HRD Score (beta)
- Identify QIAseq DNA Somatic Variants with TMB Score
- Identify QIAseq DNA Ultra Somatic Variants
- Exome and xHYB template workflows
- Create QIAseq Exome CNV Control Mapping
- Identify QIAseq Exome Causal Inherited Variants in Trio
- Identify QIAseq Exome Germline Variants
- Identify QIAseq xHYB Germline Variants
- Identify QIAseq xHYB Somatic Variants