Omics Tests¶

The Omics Tests page allows you to view the genomic tests that have been indexed/ingested into the PHC. You can filter by subject or test status.

To view test files in the Omics Explorer or Insights, you must first upload the genomic files (such as raw data, VCF, or BAM files) into the Files tab of the PHC. They are then ingested/indexed into our genomics database and associated with the correct subject.

Navigate to Omics Test page¶

The Omics Test page allows you to view and filter the omics files that have been ingested and indexed, are currently queued for indexing, or have failed. The Omics Test page can be accessed via the Omics Tab on the left panel of the PHC:

1. Click the Omics tab. This opens the Omics Dashboard and now the Add Data and Tests options are available to select under Omics in the left side panel (see image above).

2. Click on Tests on the left side panel. The Tests page opens (see image below).

   

To the left of the Test Table are filters to fine tune your search. Select from the following and then click Add Filter:

1. Subject Search by Identifier - type in box to search for a subject id
2. Type and Status
   • Data Type
     • Short Variants
     • RNA Expression
     • Structural Variants
     • Copy Number Variants
     • BAM Files
   • Test Status
     • Active
     • Indexing
     • Failed

The table to the right will update with the filtered results.

If you hover on a test, a purple pop-up will present buttons for quick access to the following (see image below):

• Open in Subject Viewer
• Open in Omics Explorer
• Open in Files UI

• Delete Test - users with the proper ABAC permissions can click this to delete a test

  Note: Clicking Delete Test only deletes the ingested data. The base file used to generate the tests still exists in the Files UI.

  

• View CLI Help - this opens a popup with a link you can copy to run in the LifeOmic CLI

• View Details - takes you to the Test Detail page. You can also get to the Test Detail page by clicking on a test row

Omics Test Detail Page¶

The Test Detail page shows all the variant & sequence types reported in the test in one Variant Sets table, as well as information about when the test occurred, was uploaded, and was ingested.

The blue header of the page has the project name, the tab of the PHC you are in, and the automated name for the test file.

Beneath the blue header on the left is the test name and subject id. The top right has buttons for quick access to:

• Open the subject in Subject Viewer
• Open the test in Omics Explorer
• Open the files in Files UI
  Note: Test files won't have readme's generated automatically, however, an admin could manually create a readme.
• View CLI Help - this opens a popup with a link you can copy to run in the LifeOmic CLI (see image below)

The three milestones map where the test is in the process (see image below):

• Test Date (user specified - if nothing is entered it defaults to uploaded date)
• Uploaded Date

• Ingestion Date - this is when it was ingested into the PHC, indexed, and added to LifeOmic's analytics

  

The Variant Sets table shows all the variant & sequence types reported in the test, allowing quick access to view all the results in one place.

Sets table info includes:

• Test Status (active , indexing , or failed )
• Sequence Type (Somatic or Germline)
• Set Type (Copy Number Variant, Structural Variant, BAM Files, RNA Expression, and Short Variants)
• Name (Ashion, Ashion RNA, 23andMe, and others)

• File - Clicking this takes you to the .vcf file to view or download it:

  • If the .vcf file is too large, you'll get the following warning (clicking the Open File button will download the file)

  

  • If the .vcf file is small enough, it will open, allowing you to read it inline (as seen in the image below).

  

The buttons in the .vcf file blue header(see image above) include:

• View CLI help
• Download it (If the file is too large, it will tell you it’s too large. You can click the “Open file” link and it will download the file to your computer.)
• Send a shareable link to this page

More information about Omics files can be found here.