Fastq to Germline CNV Control

The Fastq to Germline CNV Control template workflow produces coverage tables that can be used as controls for copy number variant detection.

The workflow can only be used with targeted data.

Use the workflow to generate coverage tables for the Fastq to Annotated Germline Variants with Coverage Analysis template workflow (Fastq to Annotated Germline Variants with Coverage Analysis).

Fastq to Germline CNV Control can be found at:

        Template Workflows | LightSpeed Workflows (Image lightspeed_wf_folder_open_16_n_p) | Fastq to Germline CNV Control (Image cnv_control_ls_16_n_p)

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.

In the first wizard step, select the target regions (figure 4.28).

The target regions must be identical to the target regions that will later be used for copy number variant detection together with the control coverage tables.

Image germline_cnv_select_targets
Figure 4.28: Select the target regions.

Next, select a Reference Data Set (figure 4.29). 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.

If none of the available reference data sets are appropriate, custom reference data sets can be created, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Custom_Sets.html.

Image germline_cnv_select_ref_data
Figure 4.29: Select a reference data set.

In the LightSpeed Fastq to Germline Variants wizard step (figure 4.30) you have the following options:

Image germline_cnv_select_fastq
Figure 4.30: Select fastq files.

In the QC for Targeted Sequencing wizard step, define the threshold for minimum coverage (figure 4.31). This threshold is important because it is used in the quality control section of the sample report. In the later wizard step for Create Sample Report, you will be able to adjust the percent bases in the target regions that should meet this threshold.

Image germline_cnv_set_coverage_threshold
Figure 4.31: Set the coverage threshold. This threshold is used in the quality control section of the sample report.

In the Create Sample Report wizard step, select relevant summary items and specify thresholds for quality control (figure 4.32). 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.

To add more summary items, press Add..., choose the report type LightSpeed fastq to germline variants or QC for targeted sequencing and select summary items as appropriate.

Image germline_cnv_create_sample_report
Figure 4.32: Specify summary items. These will be shown in the quality control section of the sample report.

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



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