QIAseq Pro Fastq to Germline Variants
The QIAseq Pro Fastq to Germline Variants template workflow supports analysis of QIAseq Targeted DNA Pro data.
It can be used to:
- Identify and annotate germline variants and generate various QC metrics.
- Identify copy number variants if control coverage tables are provided.
- Generate control coverage tables for copy number variant detection.
The workflow can be found at:
Template Workflows | LightSpeed Workflows (
) | QIAseq workflows (
) | QIAseq Targeted DNA Pro (
) | QIAseq Pro Fastq to Germline Variants (
)
Options in the following dialogs can be configured:
- Choose where to run If you are connected to a CLC Server via your 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.
- Specify the workflow path The following paths can be configured:
- Analysis options Specify whether you want to
- Analyze sample Detect variants and, optionally, CNVs.
- Create CNV control Create a CNV control coverage table from a normal sample.
- Analyze sample and create CNV control Detect variants and create a CNV control coverage table.
- Detect CNVs
- No Copy number variants will not be called.
- Yes Copy number variants will be called if control coverage tables are provided in the Copy Number Variant Detection (Targeted) dialog.
- Analysis options Specify whether you want to
- Specify reference data handling Select the relevant Reference Data Set. QIAseq DNA Pro Panels hg38 will be pre-selected and is recommended for running this workflow. If you have not downloaded the Reference Data Set yet, the dialog will offer the opportunity to download it using the Download to Workbench button. If the QIAseq DNA Pro Panels hg38 reference data set does not contain the needed primers and target regions, a custom reference data set can be created, see Reference Data Sets and defining Custom Sets. Reference data sets for QIAseq Targeted DNA and QIAseq Targeted DNA Ultra panels should not be used with this workflow. The differences in read structure will for example prevent primers from being correctly trimmed.
- LightSpeed Fastq to Germline Variants
Specify options for the LightSpeed Fastq to Germline Variants tool:
- Reads (fastq) Press Browse to select fastq files for analysis.
- Masking mode To enable reference masking when mapping reads, set this option and select a masking track.
- Masking track Provide a masking track for the chosen reference genome if reference masking has been enabled.
- Minimum average quality Specify the minimum average quality of detected variants. See Germline variant detection for additional details.
- Minimum allele count Specify the minimum number of reads supporting an identified variant.
- Batch Select if fastq files from different samples are used as input, and each sample should be analyzed individually (for information about batching see Batching).
- Join lanes when batching Select to join fastq files from the same sample that were sequenced on different lanes.
- Target regions Choose the relevant target regions from the drop down list.
- Target primers Choose the relevant target primers from the drop down list.
- QC for Targeted Sequencing Set the Minimum coverage parameter of the QC for Targeted Sequencing tool. Using default settings, samples where 90 percent of target region positions do not meet this threshold will be flagged in the sample report generated by the workflow.
- Copy Number Variant Detection (Targeted), if CNV detection is enabled. Specify Controls against which the coverage pattern in your sample will be compared in order to call CNVs. If you do not supply any controls, the CNV analysis will not be carried out. Please note that if you want the CNV analysis to be done, it is important that the controls supplied are meaningful controls for the sample being analyzed. Mapping of control samples for the CNV analysis can be done by running this workflow with Analysis options set to Create CNV control or Analyze sample and create CNV control in the dialog Specify workflow path.
A meaningful control must satisfy two conditions: (1) It must have a copy number status that is meaningful to compare against. For panels with targets on the X and Y chromosomes, the control and sample should be matched for gender. (2) The control read mapping must result from the same type of processing that will be applied to the sample. For more information about CNV detection, see Copy Number Variant Detection.
- Create Sample Report Select relevant summary items and specify thresholds for quality control. Summary items, thresholds and an indication of whether specified thresholds were met, will be shown in the quality control section of the sample report. The default summary items are appropriate for many data sets, but may need to be adjusted. For additional information, see Create Sample Report.
- 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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