Documentation : Load Samples Into VariantDB

Data can be loaded either by uploading it to an FTP server, or by sending it directly from a galaxy server.

1. FTP upload

  1. Go to : New Data in the top menu.
  2. If your system administrator has enabled ftp upload, you should see the instructions to connect to the server. It might look like:
    instructions for ftp access
  3. After uploading VCF/BAM files to FTP server, come back to the New Data page. You will now see a selection box on top containing the uploaded data:
    selection menu for vcf upload
  4. Provide the requested information and select the data files to store in VariantDB. If 'Store Datafiles' is checked, data can be loaded directly to IGV from VariantDB
  5. To load more samples at the same time, select 'Load More Samples'
  6. Select 'Load Samples Into Database'. A status screen is shown. You can safely close this screen
  7. Upon completion of the import, you will recieve an email notification

2. Import from Galaxy

  1. Install the VariantDB tool for galaxy. This is available from the toolshed here.
  2. A publicly available galaxy server with this tool installed is available here
  3. Make sure you use the EXACT same username in galaxy and VariantDB
  4. Generate a VCF file (preferably with GATK Unified Genotyper
  5. Open the 'VCF To VariantDB' tool:
  6. Provide necessary information and select execute. Import will be finished when the job finishes.