Add Data¶

Add Data allows you to manually associate genomic files that don't have any subject identifying information in the file with a subject and have them added/indexed into the PHC database for filtering and viewing in Omics Explorer and Subject Viewer. This can also be performed using the Workflow UI. Test files that have subject identifying information in them can be ingested and indexed with the automated workflow process.

The Add Data page for omics tests can be accessed by clicking the Omics tab on the left panel of PHC. The Omics Dashboard will open, and the left panel will now show options for Add Data and Tests. Be sure to click the Add Data option under the Omics tab, as the other Add Data tab (shown uncircled in the image below) does not add genomic data, rather it is a way to add a patient to the PHC.

Types of Omics Tests to Add¶

At the top of the Add Data page of the Omics tab, there is a set of five milestones to map your path. These are shown in the image above. On each milestone page, complete the requested data and click Next to advance to the next milestone.

Foundation Medicine Test¶

In the Omics Data milestone, select Foundation Medicine Test. The test XML file will be converted into a VCF file along with other CSV files to capture any copy number or structural mutations. A single omics test will be created for the subject. This option is only available for GRCh37 projects.

In the File milestone, fill out the following:

1. Test XML File: click on the icon (looks like an edit icon) to navigate to the file
2. Test Name: Give the test a name (this will be displayed on the dashboard and Omics Explorer)
3. Test Type: Tell what type of Foundation Medicine test was performed (such as Heme)
4. Test Date: Date and time test was performed
5. Click Next

In the Subject milestone:

1. Select the existing subject that should own this omics data (click in the search box to search for subjects by identifier – you can scroll through a list of all subjects in the project)
2. Click Next

In the Confirm milestone:

1. Confirm the settings for the file are correct
2. Click Start to begin the indexing process

Ashion GEM ExTra Test¶

In the Omics Data milestone, select Ashion GEM ExTra Test. The relevant files will be extracted and processed from the GEM ExTra TAR file. A single omics test will be created for the subject. This option is only available for GRCh37 projects.

In the File milestone, fill out the following:

1. Test TAR file: Click the icon to open a popup where you can search for a file
2. Test Date: The date and time when the test was performed

In the Subject milestone:

1. Select the existing subject that should own this omics data (Click in the search box to search for subjects by identifier or scroll through a list of all subjects in the project.)
2. Click Next

In the Confirm milestone:

1. Confirm the settings for the file are correct
2. Click Start to begin the indexing process

Custom Omics Test¶

In the Omics Data milestone, select Custom Omics Test. Fill out all pertinent information. Add raw omics files like VCFs and BAMs to a project. A single omics test will be created for the subject.

In the File milestone (shown above) complete the following:

1. Test Name: This name will be displayed on the Dashboard and Omics Explorer
2. Test Type: The type of test that was performed
3. Sequence Type: Select from Genomic or Somatic
4. Test Date: The date and time when the test was performed
5. Variant Call Format (VCF) file: Click the icon to open a popup where you can search for a file
6. Sequence Alignment Map (BAM) file: Click the icon to open a popup where you can search for a file
7. RNA Expression CSV file: Click the icon to open a popup where you can search for a file
8. Copy Number CSV file: Click the icon to open a popup where you can search for a file
9. Structural Variant CSV file: Click the icon to open a popup where you can search for a file. Look at Data Processing for information on how to format CSV files for proper ingestion.
10. Click Next

In the Subject milestone:

1. Select the existing subject that should own this omics data(Click in the search box to search for subjects by identifier or scroll through a list of all subjects in the project.)
2. Click Next

In the Confirm milestone:

1. Confirm the settings for the file are correct
2. Click Start to begin the indexing process

Once you’ve started the indexing, you can return to the Omics Dashboard to check the file status (indexing/active/failed).