Subsections

Identify Causal Inherited Variants in Trio (TAS)

The Identify Causal Inherited Variants in a Trio (TAS) ready-to-use workflow identifies putative disease causing inherited variants by creating a list of variants present in both affected individuals and subtracting all variants in the unaffected individual. The workflow includes a back-check for all family members.

Run the Identify Causal Inherited Variants in a Trio (TAS) workflow

To run the Identify Causal Inherited Variants in a Trio (TAS) workflow, go to:

        Toolbox | Ready-to-Use Workflows | Targeted Amplicon Sequencing Sequencing (Image targeted_sequencing_closed_16_n_p) | Hereditary Disease (Image hereditary_folder_closed_16_n_p) | Identify Causal Inherited Variants in a Trio (TAS) (Image causal_inherited_variant_trio_tas_16_n_p)

  1. Double-click on the Identify Causal Inherited Variants in a Trio (TAS) 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. The sequencing reads from the different family members are specified one at a time in successive dialogs (figure 15.54).

    The sequencing reads from the different family members are specified one at a time in the appropriate window. The panel in the left side of the wizard shows the kind of input that should be provided. Select by double-clicking on the reads file name or click once on the file and then on the arrow pointing to the right side in the middle of the wizard.

    Image reads_iciv3_tas
    Figure 15.54: Specify the sequencing reads for the appropriate family member.

  3. Select the targeted region file (figure 15.55).

    The targeted region file is a file that specifies which regions have been sequenced, when working with whole exome sequencing or targeted amplicon sequencing data. This file is something that you must provide yourself, as this file depends on the technology used for sequencing. You can obtain the targeted regions file from the vendor of your targeted sequencing reagents.

    Image targetedregions_iciv3_tas
    Figure 15.55: Select the targeted region file you used for sequencing.

  4. Select which reference data set should be used to identify causal inherited variants (figure 15.56).

    Image identify_causalinherited_variantstrio_tas
    Figure 15.56: Choose the relevant reference Data Set to identify causal inherited variants.

  5. Specify the Hapmap populations that should be used for filtering out variants found in the Hapmap database (figure 15.57).

    Image removehapmap_iciv3tas
    Figure 15.57: Select the relevant Hapmap population(s).

  6. Specify the parameters for the Fixed Ploidy Variant Detection tool for each family member successively (figure 15.58).

    The parameters used by the Fixed Ploidy Variant Detection tool can be adjusted. We have optimized the parameters to the individual analyses, but you may want to tweak some of the parameters to fit your particular sequencing data. A good starting point could be to run an analysis with the default settings.

    Image fp_settings_iciv3_tas
    Figure 15.58: Specify the parameters for the Fixed Ploidy Variant Detection tool.

    The parameters that can be set are:

    • Required variant probability is the minimum probability value of the 'variant site' required for the variant to be called. Note that it is not the minimum value of the probability of the individual variant. For the Fixed Ploidy Variant detector, if a variant site - and not the variant itself - passes the variant probability threshold, then the variant with the highest probability at that site will be reported even if the probability of that particular variant might be less than the threshold. For example if the required variant probability is set to 0.9 then the individual probability of the variant called might be less than 0.9 as long as the probability of the entire variant site is greater than 0.9.
    • Ignore broken pairs: When ticked, reads from broken pairs are ignored. Broken pairs may arise for a number of reasons, one being erroneous mapping of the reads. In general, variants based on broken pair reads are likely to be less reliable, so ignoring them may reduce the number of spurious variants called. However, broken pairs may also arise for biological reasons (e.g. due to structural variants) and if they are ignored some true variants may go undetected. Please note that ignored broken pair reads will not be considered for any non-specific match filters.
    • Minimum coverage: Only variants in regions covered by at least this many reads are called.
    • Minimum count: Only variants that are present in at least this many reads are called.
    • Minimum frequency: Only variants that are present at least at the specified frequency (calculated as 'count'/'coverage') are called.

  7. Specify the parameters for the QC for Targeted Sequencing tool for for each family member successively (figure 15.59).

    When working with targeted data (WES or TAS data), quality checks for the targeted sequencing is included in the workflows. Again, you can choose to use the default settings, or you can choose to adjust the parameters.

    Image qc_settings_iciv3_tas
    Figure 15.59: Specify the parameters for the QC for Targeted Sequencing tool.

    The parameters that can be set are:

    • Minimum coverage provides the length of each target region that has at least this coverage.
    • Ignore non-specific matches: reads that are non-specifically mapped will be ignored.
    • Ignore broken pairs: reads that belong to broken pairs will be ignored.

  8. 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.

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

Output from the Identify Causal Inherited Variants in a Trio (TAS) workflow

The following outputs are generated: