Set Analysis Parameters

Set Analysis Parameters

1. Launch the app from BaseSpace Sequence Hub.
  1. Select the Apps tab.
  2. Select TruSight Tumor 170.
  3. From the drop-down list, select version 2.0.0, and then select Launch Application.
2. [Optional] In the Analysis Name field, enter an analysis name of your preference.

The default is the app name followed by the date and time the analysis session started.

3. Select the Select Project button.
4. In the Select Project dialog box, do one of the following:
Select an existing project to store the app results.
Select New to create a project. Add a name and description, and select Create to add it to the projects list.
5. Select Select in the Select Project dialog box.
6. For DNA Intermediate Files, select which BAM files to keep from the following options:
Keep aligned and realigned BAM files.
Keep aligned BAM files only.
Keep realigned BAM files only.
Do not keep any BAM files.

The analysis generates a set of BAM files after alignment and a second set of BAM files after indel realignment. Deleting BAM files may reduce long‑term data storage costs. It is not possible to delete individual BAM files from the app results.

7. Select Select Pairs to select samples for a pair.
8. Select samples to analyze, and drag them to either the DNA or RNA column. Select Filters to filter the Samples list by project.
Pairs must have equivalent read lengths.
The analysis results from pairs are in the Combined Variant Report.
The maximum number of samples is 16.
DNA and RNA samples can be analyzed individually.
9. When sample selection is complete, select Confirm.
10. Select Launch Application.

When the analysis completes, the app session status automatically updates.