Set Analysis Parameters

Set Analysis Parameters

1 In BaseSpace, click the Apps tab.
2 Click TruSeq Amplicon.
3 From the drop-down list, select version 2.0, and then click Launch to open the app.
4 In the Analysis Name field on the app input form, enter the analysis name.

By default, the analysis name includes the app name, followed by the date and time that the analysis session starts.

5 From the Save Results To field, select the project that stores the app results.
6 From the Sample(s) field, browse to the sample you want to analyze and select the checkbox. You can select multiple samples.
7 From the Targeted Amplicons field, select a panel of targeted amplicons representative of the selected samples.
8 If you selected Custom Panel in the Targeted Amplicons drop-down list, upload a custom manifest and select the manifest file from the Custom Manifest File field. Upload a custom manifest as follows.
    a Navigate to your project in BaseSpace.
    b Click Import.
    c Follow the instructions to add the Custom Amplicon manifest file (*.txt) to the project.

Note

Specify the reference genome in the header of the manifest file. See Reference Genomes.

9 From the Variant Caller field, select a variant caller.

For tumor samples, use the Somatic Variant Caller.

10 If using the somatic variant caller, specify the Somatic Variant Caller Threshold (percentage).

Set to 5 by default. Variants with a frequency below the specified threshold are not reported in VCF files. Lower threshold values can result in false positive variants.

11 Set the Read Stitching option.

When enabled, reads that overlap > 10 bases between Read 1 and Read 2 are combined to create a single (longer) read for alignment.

12 From the Annotation field, select a preferred gene and transcript annotation reference database.
13 Click Continue.

The TruSeq Amplicon App begins analysis of the sample.

When analysis is complete, the status of the app session is updated automatically and an email is sent to notify you.