How to run the Filter Causal Variants (WES-HD) workflow

To run the Filter Causal Variants (WES-HD) workflow, go to:

        Toolbox | Ready-to-Use Workflows | Whole Exome Sequencing (Image exome_sequencing_closed_16_n_p) | Hereditary Disease (Image hereditary_folder_closed_16_n_p) | Filter Causal Variants (WES -HD) (Image filter_somatic_var_wes_16_n_p)

  1. Double-click on the Filter Somatic Variants (WES-HD) tool to start the analysis. If you are connected to a server, you will first be asked where you would like to run the analysis.

  2. Select the variant track you want to use for filtering causal variants (figure 13.48).

    The panel in the left side of the wizard shows the kind of input that should be provided. Select by double-clicking on the variant track name or click once on the file and then click on the arrow pointing to the right side in the middle of the wizard.

    Image filtervariant_filtercausalweshd
    Figure 13.48: Select the variant track from which you would like to filter somatic variants.

  3. Specify which of the 1000 Genomes populations should be used for annotation (figure 13.49).

    Image 1000genomes_filtercausalweshd
    Figure 13.49: Select the relevant 1000 Genomes population(s).

  4. Specify the 1000 Genomes population that should be used for filtering out variants found in the 1000 Genomes project. This can be done using the drop-down list found in this wizard step. Please note that the populations available from the drop-down list can be specified with the Data Management (Image search_database_16_h_p) function found in the top right corner of the Workbench (see Download and configure reference data).

  5. Specify the Hapmap populations that should be used for filtering out variants found in Hapmap (figure 13.50).

    This can be done using the drop-down list found in this wizard step. Please note that the populations available from the drop-down list can be specified with the Data Management (Image search_database_16_h_p) function found in the top right corner of the Workbench (see Download and configure reference data).

    Image removehapmap_filtercausalwes
    Figure 13.50: Select the relevant Hapmap population(s).

  6. Pressing the button Preview All Parameters allows you to preview all parameters. At this step you can only view the parameters, it is not possible to make any changes. Choose to save the results and click on the button labeled Finish.