Using the Genomes Page

Charlene Son-Rigby -

The Genomes page lists all the genomes in a project, as well as all reports that have been run on the genomes. All genomes have a Variant Report, which is the output of the Opal Annotation Engine. Any VAAST or Flex analyses that have been run will be listed as well.

Navigation

You can reach the Project Genomes View from:
-  Opal Home page  >>  Projects link  >>  Project Name
-  Opal Toolbar  >>  Menu dropdown >>  Projects option  >>  Project Name

Features

Genomes Table

The Genomes table provides the following information for each genome:

Genome Label
Short descriptive name for the genome, which is specified during upload in the Upload Genome dialog box. Click on the Genome Label to display the Genome Info window with meta-data for the genome.
Clinical Grade
Clinical Grade
This field provides information regarding the quality of genome variant file. The quality is indicated by the signal-strength icon. The higher the quality, the more “bars” the icon shows. Click on the icon for more detailed metrics on the Clinical Grade for this genome.
ROH
Click to review the Regions of Homozygosity within the sample. The Regions of Homozygosity (ROH) viewer highlights whether your genome contains any large regions of homozygosity.  You can specify the cutoff for the size of the regions that you are interested in seeing: >5MB, >3MB, or >1MB.
Uploaded On
Date the genome variant file was uploaded.
Report Type
Opal produces several types of reports including Variant Reports, VAAST Reports and Flex Reports. Click the X icon to delete a report. Click on the Report Type to open the report and review the variants.
Variant Report
This is the primary annotation report generated when uploading a genome. A warning symbols behind the Variant Report indicates a problem with the uploaded VCF file.
 The report contains variants that failed.
 The report contains variants that were altered. The Variant Report has the Status Complete and can be used to launch VAAST report or Clinical Reports.
 The VCF file could not be processed successfully. The Variant Report has the Status Failed.
Clicking on the warning symbol opens the Variant Report Errors/Warnings dialog box.
VAAST Report
Phevor Report
FLEX Report
Report Date
A timestamp reporting the date when the report was generated.
Version
Version of the annotation engine or analysis workflow used to generate the report. For annotation reports, click on the hyperlink to review the Annotation Pipeline Database and Algorithm Versions used.
Status
Indicates the status of the genome in the annotation pipeline: Submitted, Running, Complete, or Failed.

Actions

The following actions are available on this page:

Launch App
From this dropdown menu you can launch a pre-configured advanced analysis workflow such as VAAST from the App Store directly from within your project. For more information on the advanced analysis workflows please see Advanced Genome Analysis Using VAAST and Phevor and Advanced Genome Analysis Using Flex.
Actions
Depending on your Project Role and Workspace Role you can choose the following actions from the dropdown menu:
Project Details
View the Project Description and the list of Contributors and Viewers.
Edit Project
Opens the Edit Project dialog box to update the project details and change default project sharing settings.
Share Project
Opens the Share Project dialog box to change the Project Roles individually for each user.
Upload Genomes
Opens the Upload Genome dialog box to add new genomes to the project.
Rename Genomes
Allows you to change the Genome Label for genomes. Select the genomes in the Genomes table by checking the box in front of their Genome Label, then select Rename Genomes from the Actions menu to open the Rename Selected Genomes dialog box. Enter the new labels and click Rename Genome(s) to save.
Move Genomes
Allows you to move selected genomes to another project in the workspace. Select the genomes from the Genomes table by checking the box in front of their Genome Label, then select Move Genomes from the Actions menu to open the Move Selected Genomes dialog box. Select the target project from the dropdown menu and click Move Genome(s) to save.
Note: You cannot move genomes to another Workspace.
Delete Genomes
To delete genomes select the genomes from the Genomes table by checking the box in front of their Genome Label, then select Delete Genomes from the Actions menu to open the Delete Selected Genomes dialog box. You are prompted to confirm or cancel the deletion. This will delete the genome and any associate reports.

 

 

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