Uploading a Genome

Charlene Son-Rigby -

The Upload Genome page enables you to upload variant files in VCF format. Both single and multi-genome vcf files are supported. Multi-genome vcf files will be split into individual genomes before submitting to the pipeline.

Navigation

You can reach the Upload Genome page from:
-  Opal Home page  >>  Upload Genome link
-  Opal Toolbar  >>  Menu dropdown >>  Upload Genome option
-  Opal Toolbar  >>  Upload Genome link
-  Projects page >> Action menu >> Upload Genome

Elements

To upload a genome, provide the following information:

Project (required)
Specify the project to organize the genome into by:
-  selecting an existing project from the dropdown menu or
-  clicking “+ New Project” to create and select a new project 
When navigating to the Upload Genome page from a project's Actions menu on the Projects page that project is preselected as the default project.
Variant File (required)
Click the “Choose File” button to open a file picker and select a genome variant file on your computer or file system.
Note: Compress your variant files to save space and reduce upload time. The supported compressed file formats are zip, gzip, and bzip2.
Genome Label
Enter a short, unique non-personally identifying label for the genome. When uploading a multi-sample vcf file the provided Genome Label will be appended by the genome names in the vcf header line. The Genome Label can be edited later by renaming the genome.
External ID
Use the External ID to keep track of your organization's identifier for this genome, e.g. record ID in your LIMS system. The External ID can be edited later by renaming the genome.
Sex
Select  Male, Female, or Unspecified. The Sex cannot be edited after the genome upload. 
Variant File Format
VCF is preselected, currently this is the only format supported. 
Confirm your Assembly Version (required)
Check the checkbox to confirm the assembly version for your genome. Currently only GRCh37/hg19 is supported.
Upload
Click this button to begin the upload process. Upload takes a few seconds to a few minutes depending on the size of the file and your network speed.
Reset
Sets this form to the default values.

When the upload is completed your genome will automatically be submitted to the Opal Annotation Engine. Opal Annotation Engine v4 is a comprehensive annotation pipeline that appends gene and impact information, multiple predictive scores, as well as links to literature evidence. The architecture includes a robust, fully scalable processing engine that processes genomes in under an hour and exomes in just a few minutes.

Your resulting Variant Report will be ready for review as soon as your sequence file is processed.

Notifications

When the processing of your sequence file is completed successfully a message with a link to your project is displayed at the bottom of the Upload Genome page when still on the page. You will also receive an email notification when the Variant Report is ready.

If your genome variant file does not comply with Fabric Genomics' variant file format guidelines, the notifications will provide you with some information regarding the processing of the file. Please verify that your file complies with the specified formats, make any necessary changes, and re-submit the file. See Appendix 1 for more information on supported genome variant file formats.

Have more questions? Submit a request

Comments