How to run the Identify Somatic Variants from Tumor Normal Pair (WES)

  1. Go to the toolbox and double-click on the Identify Somatic Variants from Tumor Normal Pair (WES) ready-to-use workflow. This will open the wizard shown in figure 14.22 where you can select the tumor sample reads.

    Image filter_somatic_variants_from_tumor_normal_step1_wes
    Figure 14.22: Select the tumor sample reads.

    When you have selected the tumor sample reads click on the button labeled Next.

  2. In the next wizard step (figure 14.23), please specify the normal sample reads.

    Image filter_somatic_variants_from_tumor_normal_step2_wes
    Figure 14.23: Select the normal sample reads.

  3. The following 2 steps allow you to restrict the calling of indels and structural variants to the targeted regions, both for tumor and normal reads (figure 14.24).

    Image filter_somatic_variants_from_tumor_normal_step3_wes
    Figure 14.24: Specify the target regions track.

  4. Set the parameters for the Low Frequency Variant Detection step (figure 14.25) and click Next.

    Image filter_somatic_variants_from_tumor_normal_step4_wes
    Figure 14.25: Specify the settings for the variant detection.

  5. In the following 2 wizard steps, you can select your target regions track to be used for reporting the performance of the targeted re-sequencing experiment for the tumor and normal samples successively (figure 14.26). The targeted region track should be the same as the track you selected in the previous wizard steps. Variants found outside the targeted regions will not be included in the output that is generated with the ready-to-use workflow.

    Image filter_somatic_variants_from_tumor_normal_step5_wes
    Figure 14.26: Select your target region track.

  6. Next, adjust the settings for removal of germline variants step (figure 14.27). Click on the button labeled Next.

    Image filter_somatic_variants_from_tumor_normal_step6_wes
    Figure 14.27: Select your target region track.

  7. In the next wizard step you can check the selected settings by clicking on the button labeled Preview All Parameters (figure 14.28).

    Image filter_somatic_variants_from_tumor_normal_step10_wes
    Figure 14.28: Check the parameters and save the results.

    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. At the bottom of this wizard there are two buttons regarding export functions; one button allows specification of the export format, and the other button (the one labeled "Export Parameters") allows specification of the export destination. When selecting an export location, you will export the analysis parameter settings that were specified for this specific experiment.

  8. Click on the button labeled OK to go back to the previous wizard step and choose Save.