Run the Filter Causal Variants (TAS-HD) workflow

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

        Toolbox | Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | Targeted Amplicon Sequencing (Image targeted_sequencing_closed_16_n_p) | Hereditary Disease (Image hereditary_folder_closed_16_n_p) | Filter Causal Variants (TAS-HD) (Image filter_somatic_var_tas_16_n_p)

  1. Double-click on the workflow name 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 21.43).

    Image filtervariant_filtercausaltashd
    Figure 21.43: Select the variant track from which you would like to filter somatic variants.

  3. In the next dialog, you have to select which data set should be used to filter causal variants (figure 21.44).

    Image filtercausal_variants_tas
    Figure 21.44: Choose the relevant reference Data Set to annotate.

  4. The 1000 Genomes population(s) is bundled in the downloaded reference dataset and therefore preselected in this step. If you want to use another variant track you can browse in the navigation area for the preferred track (figure 21.45).

    Image 1000genomes_filtercausaltashd
    Figure 21.45: Use the preselected 1000 Genomes population(s) or select another variant track.

  5. Specify the Hapmap populations that should be used for filtering out variants found in Hapmap (figure 21.46).

    Image removehapmap_filtercausaltashd
    Figure 21.46: Select the relevant Hapmap population(s).

  6. In the last wizard step you can check the selected settings by clicking on the button labeled Preview All Parameters. In the Preview All Parameters wizard you can only check the settings, and if you wish to make changes you have to use the Previous button from the wizard to edit parameters in the relevant windows.

  7. Choose to Save your results and click on the button labeled Finish.