Add VCF files

A single- or multi-sample VCF file can be annotated and added to a GenVision Pro session as long as you also have the same version reference sequence. Though the workflow takes place within GenVision Pro, the SeqMan NGen wizard is used to set up the job and run it behind the scenes.

During the importation of these files, GenVision Pro automatically performs variant calling, allowing you to later create tables of variants and structural variations and to view variants in the Analysis view.

To add a VCF file to a GenVision Pro session:

1. Do any of the following:
   
   
   • From the New tab of the Welcome screen, choose Add VCF variants to new session.
     
     
   • From the main menu, choose File > Add VCF.
     
     
   • Near the top of the GenVision Pro window, click the Add VCF to Session tool ( ).

2. The SeqMan NGen wizard opens at the Set Up VCF screen. Enter information and upload file(s) to the screen as prompted.
   
   
   
   
   • Use the Add button to navigate to the VCF file(s) you want to add to the session.
     
     
   • By default, only variants that pass the current set of multi-sample variant filters will be included. (optional) To instead include all variants, uncheck the box.
     
     
   • Enter a name in the Project name box.
     
     
   • Click Browse to browse to a folder where the project should be saved.

3. Click Run. The wizard closes automatically and the annotation step begins.

4. (optional) Check the progress of the run in the Jobs panel. Even for large projects such as the human genome, annotating and adding a VCF file typically takes 5 minutes or less.
   
   

At the conclusion of the run, the annotated VCF files will appear in the Experiments section of the Explorer panel. In the Tracks panel, additional Alignment and Variants tracks are now available in the Analysis body section and can be applied to the Analysis view, if desired.