Subsections

Run the Identify Variants (TAS) workflow

  1. To run the Identify Variants (TAS) template workflow, go to:

            Workflows | Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | Targeted Amplicon Sequencing (Image targeted_sequencing_closed_16_n_p) | Somatic Cancer (Image somatic_folder_closed_16_n_p) | Identify Variants (TAS) (Image identify_variants_tas_16_n_p)

  2. Select the sequencing reads from the sample that should be analyzed (figure 20.27).

    Image identify_variants_wizardstep1_tas
    Figure 20.27: Please select all sequencing reads from the sample to be analyzed.

    If several samples should be analyzed, the tool has to be run in batch mode. This is done by checking "Batch" and selecting the folder that holds the data you wish to analyze.

  3. In the Target regions dialog you specify the target regions for your application (figure 20.28). The variant calling will be restricted to these regions.

    Image identify_variants_wizardstep2_tas
    Figure 20.28: Select the track with the targeted regions from your experiment.

  4. In the next dialog, you have to select which reference data set should be used to identify variants (figure 20.29).

    Image identify_variants_tas
    Figure 20.29: Choose the relevant reference Data Set to identify variants in your sample.

  5. In the next wizard step (figure 20.30) you can specify the parameters for variant detection.

    Image identify_variants_wizardstep3_tas
    Figure 20.30: Specify the parameters for variant detection.

  6. In the next wizard step (figure 20.31) you specify the parameters for the QC reporting on the targeted regions.

    Image identify_variants_wizardstep4_tas
    Figure 20.31: Specify minimum coverage for the QC reporting on the targeted regions.

  7. 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.

  8. Choose to Save your results and click Finish.

Output from the Identify Variants (TAS) workflow

The Identify Variants (TAS) tool produces five different types of output:

It is important that you do not delete any of the produced files individually as some of the outputs are linked to other outputs. If you would like to delete the outputs, please always delete all of them at the same time.

First have a look at the mapping report to see if the coverage is sufficient in regions of interest (e.g. > 30 ). Furthermore, check that at least 90% of reads are mapped to the human reference sequence. In case of a targeted experiment, also check that the majority of reads are mapping to the targeted region.

Afterwards please open the Genome Browser View file (see  20.32).

The Genome Browser View includes the track of identified variants in context to the human reference sequence, genes, transcripts, coding regions, targeted regions and mapped sequencing reads.

Image identify_variants_result1_tas
Figure 20.32: The Genome Browser View allows you to inspect the identified variants in the context of the human genome.

Open the variant track as a table to see information about all identified variants (see 20.33).

Image identify_variants_result2_tas
Figure 20.33: Genome Browser View with an open track table to inspect identified variants more closely in the context of the human genome.