Fastq to Annotated Germline Variants

The Fastq to Annotated Germline Variants template workflow identifies germline variants and annotates these with exon number and amino acid changes.

The workflow can be used to identify and annotate variants in both targeted sequencing and whole genome sequencing pipelines.

The workflow can be found at:

        Template Workflows | LightSpeed Workflows (Image lightspeed_wf_folder_open_16_n_p) | Fastq to Annotated Germline Variants (Image annotate_variants_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 a Reference Data Set (figure 4.1). 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 fagv_select_ref_data
Figure 4.1: Select a reference data set.

In the LightSpeed Fastq to Germline Variants wizard step (figure 4.2) you have the following options:

Image lis_workflow_germline_step2
Figure 4.2: Select fastq files.

In the Create Sample Report wizard step, select relevant summary items and specify thresholds for quality control (figure 4.3). 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 and select summary items as appropriate.

Image fagv_create_sample_report
Figure 4.3: 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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