Filter Causal Variants (WGS-HD)

If you are analyzing a list of variants, you can use the Filter Causal Variants (WGS-HD) template workflow to remove variants that are outside the target region, as well as common variants present in publicly available databases. The workflow will annotate the remaining variants with gene names, conservation scores, and information from relevant databases.

Run the Filter Causal Variants (WGS-HD) workflow

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

        Toolbox | Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | Whole Genome Sequencing (Image whole_genome_folder_closed_16_n_p) | Hereditary Disease (Image hereditary_folder_closed_16_n_p) | Filter Causal Variants (WGS-HD) (Image filter_somatic_var_wgs_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 19.29).

    Image filtervariant_filtercausalwgshd
    Figure 19.29: 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 19.30).

    Image filtercausal_variants_wgs
    Figure 19.30: 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 19.31).

    Image 1000genomes_filtercausalwgshd
    Figure 19.31: 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 19.32).

    Image removehapmap_filtercausalwgs
    Figure 19.32: 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.

Output from the Filter Causal Variants (WGS-HD) workflow

The following outputs are generated: