Identify DNA Germline Variants workflow

When running an analysis to detect variants in DNA-seq data it is essential to include tools that allow detection of variants with high accuracy. Here we provide a basic workflow for identification of germline variants in DNA-seq data which includes the minimal number of tools that should be used for variant detection as well as a few tools to provide reports and visualization.

Please note that the tools in this workflow have not been optimized for any specific application. It is recommended that samples with known variants are used to test the secondary analysis workflow to confirm that settings in the individual tools are appropriate.

The workflow must be configured with a reference sequence. When the workflow is started, any available reference can be chosen, including reference sequences in the reference data sets that are available for download under References (QIAGEN Sets). Alternatively, the reference sequence can be specified in a copy of the workflow. All species can be used as long as the reference sequence is available.

The tools and outputs provided by this workflow are:

You find the workflow here:

        Toolbox | Template Workflow | Basic Workflow Designs (Image basic_twf_folder_closed_16_n_p) | Identify DNA Germline Variants (Image germline_variant_calling_twf_16_n_p)

To run the workflow use the start button and follow the steps that are provided in the wizards.

  1. Select the reads and click Next.
  2. Select your reference data set or select "Use the default reference data" if you want to specify a reference in the next wizard step, see figure 12.47. Read more about creating reference data in Custom Sets.
  3. Specify how the reads should be trimmed.
  4. If the data is from a targeted sequencing experiment, you can choose restrict to InDels and Structural Variants to call variants in target regions by providing a target regions file, see figure 12.48.
  5. If the data is from a targeted sequencing experiment, you can choose restrict Fixed Ploidy Variant Detection to call variants in target regions by providing a target regions file and click Next.
  6. Specify threshold for filtering variants, see figure 12.49.
  7. Finally select a save location and press Finish.

Image dna_germline_wf_select_reference_data
Figure 12.47: Wizard step for specifying reference data.

Image dna_germline_wf_select_target_region
Figure 12.48: Optional wizard step for selecting a target region.

Image dna_germline_wf_set_filtering_criteria
Figure 12.49: Wizard step for specifying variant filtering criteria.

Identify DNA Germline Variants represents the minimal number of tools that should be used for variant detection. Depending on the application, additional steps or alternative configurations may be helpful. To adapt the workflow, you must create your own copy of the workflow by right clicking on the workflow name and choosing Open Copy of Workflow. Read about creating and modifying workflows in Creating a workflow and the following sections.