2. New Project WorkflowΒΆ

This tutorial begins by opening a new instance of VarSeq and selecting Create New Project. With the Homo sapiens (Human), GRCh37 (hg19) (Feb 2009) Genome Assembly chosen, select the template called ACMG Guidelines Trio Template and then for the Name enter ACMG Trio Tutorial. If desired, you can also change the directory in which the project is stored by clicking on the Browse icon. The interface should look like Figure 2-1.

New Project 1

Figure 2-1: New project dialog.

Selecting OK brings you to the next screen that directs the user to import variants. Select Add Files, navigate to the location of the extracted ZIP file, and add select the ACMG Guidelines Trio Samples. Click Next.

Import variant wizard dialog

Figure 2-2: Import variants wizard opening screen.

In the Import Variants of Family Samples dialog, you need to define sample relationships and affection status as well as sex. For the proband (NA19240) you will need to define mother (NA12938) and father (NA12939) as well as the Affection status. You can do this by clicking on the dropdown options under the Mother and Father columns and selecting the appropriate samples. Affection status can be selected by clicking once on the box. The proband is also a Female, which should be selected under the Sex column. Mother and father Sex should also be defined. The dialog should look like Figure 2-3. Once the sample relationships are defined, you also have the option to associate BAM files using the Associate BAM File icon. Although we do not have BAM files for this project, this feature will automatically detect the BAM files if they have the same sample name and are located in the same directory or sub-directory as the VCF files. Click Next.

Import family pedigree

Figure 2-3: Defining family structure.

In the last import dialog, leave the default options selected and select Finished. This will import the VCF files into the project template.

Import variants default parameters

Figure 2-4: Leaving default paramters in import wizard.