Identify QIAseq Exome Germline Variants

The Identify QIAseq Exome Germline Variants template workflow calls germline variants.

It can be found at:

        Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | QIAseq Sample Analysis (Image qiaseqrna_folder_closed_16_n_p) | QIAseq DNA workflows (Image qiaseq_workflows_folder_closed_16_n_p) | Identify QIAseq Exome Germline Variants (Image qiaseq_germline9)

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.

In the "Select Reads" wizard step, specify the data to be analyzed (figure 13.53). This workflow expects sequencing reads as input. When selecting data from the Navigation Area, these would normally be supplied as sequence lists.

Image select_reads_exome_germline
Figure 13.53: Select the data to analyze.

The following dialog helps you set up the relevant Reference Data Set. If you have not downloaded the Reference Data Set yet, the dialog will suggest the relevant data set and offer the opportunity to download it using the Download to Workbench button. (See figure 13.54).

Image select_reference_exome_germline
Figure 13.54: The relevant Reference Data Set is highlighted. To the right, the types of reference data needed by the workflow are listed.

Note that if you wish to Cancel or Resume the Download, you can close the template workflow and open the Reference Data Manager where the Cancel, Pause and Resume buttons are available.

If the Reference Data Set was previously downloaded, the option "Use the default reference data" is available and will ensure the relevant data set is used. You can always check the "Select a reference set to use" option to be able to specify another Reference Data Set than the one suggested.

In the Map Reads to Reference dialog, it is possible to configure masking. A custom masking track can be used, but by default, the masking track is set to GenomeReferenceConsortium_masking_hg38_no_alt_analysis_set, containing the regions defined by the Genome Reference Consortium, which serve primarily to remove false duplications, including one affecting the gene U2AF1. Changing the masking mode from "No masking" to "Exclude annotated" excludes these regions.

In the Fixed Ploidy Variant Detection wizard step, the variant detection options can be configured (figure 13.55). These are:

Image exome_germline_fixedploidy
Figure 13.55: Specify the parameters for the Fixed Ploidy Variant Detection tool.

Image exome_germline_cnv
Figure 13.56: Specify the parameters for the Copy Number Variant Detection tool.

The dialog for Copy Number Variant Detection allows you to specify a control mapping against which the coverage pattern in your sample will be compared in order to call CNVs. If you do not specify a control mapping the Copy Number Variation analysis will not be carried out (figure 13.56).

Please note that if you want the copy number variation analysis to be done, it is important that the control mapping supplied is a meaningful control for the sample being analyzed. Mapping of control samples for the CNV analysis can be done using the workflow described in Create QIAseq Exome CNV Control Mapping.

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.

In the next two dialogs individual filtering settings can be specified for SNVs and indels.

In the final wizard step, choose to Save the results of the workflow and specify a location in the Navigation Area before clicking Finish.

Launching using the QIAseq Panel Analysis Assistant

The workflow is also available in the QIAseq Panel Analysis Assistant (see QIAseq Panel Analysis Assistant) under Exome.