8. Finishing Project and Saving as TemplateΒΆ

To wrap up this tutorial, we will save this project and also save it as a template that can be reused on other samples.

Much more analysis can be performed in VarSeq, however, we hope this was a good orientation to most of the functionality of the filter chain and how to annotate variants and perform computation on sources.

  1. To save the project, either:

    • Go to File > Save Project, or
    • Click on the Save Project icon on the tool bar, or
    • Use the keyboard shortcut <CTRL> + S.
  2. To save the project as a template, go to File > Save Project as Template....

    Suggested information that can be filled in the text boxes is shown in the image below and also in the bulleted list that you can copy and paste into the dialog. See Figure 8-1.

    Save as Template

    Figure 8-1: Save project as template dialog with suggested information

    • Name: Cancer Gene Panel Tutorial Template
    • Description: This template takes multiple cancer gene panel samples, performs quality filtering, variant allele frequency filtering, identifies variant in COSMIC, performs transcript annotation.
    • Series Name: Cancer Template
    • Version: 1.4.2
    • Author: Golden Helix, Inc. (or your name)
    • Tags: cancer
    • Specific Assembly: Check this box and make sure the assembly is set to Homo sapiens (Human), GRCh37 g1k (Feb 2009)

    Once this information is set click Save.

Congratulations! You have completed the Cancer Gene Panel Tutorial. If you had any problems or have any questions please feel free to contact us at support@goldenhelix.com.