Upload to QCI Interpret

The Upload to QCI Interpret tool uploads a sample to QCI Interpret or QCI Interpret Translational from several types of tracks and reports.

To run Upload to QCI Interpret:

        Toolbox | QIAseq Panel Expert Tools (Image qiaseq_expert_folder_closed_16_n_p) | QCI Interpret Integration (Image qcii_integration_folder_closed_16_h_p) | Upload to QCI Interpret (Image upload_qci_16_h_p)

In the tool wizard, choose which elements to upload and how to log in.

The first step is to define how the QCI Interpret sample will look in QCI:

The second step defines which elements will be part of the sample:

The next step defines how the uploaded VCF will be created. The Prefill VCF settings changes the VCF settings to suggested defaults depending on the data. The somatic and germline/hereditary workflows of QCI Interpret focus on different needs, with somatic being primarily focused on therapeutic, prognostic, and diagnostic actionability, while germline/hereditary is better suited for disease diagnosis/risk. Read more about VCF export settings in http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Export_in_VCF_format.html.

Image upload_qci_login
Figure 14.1: Choosing QCI region and log in.

In the final step choose your QCI Region and how to log in. See figure 14.1. To log in using a browser, choose the Browser option, then click the Log in button to open a new browser (or new tab) where you can log in, and give the workbench permission to upload samples to QCI on your behalf. To upload with API key you need an API user account, please send an email to [email protected] and ask for an API-enabled QCI Interpret account. The license team can then send you your API Key ID and API Key Secret.

Note: Do not share workflows that contain your QCI Interpret login information. A workflow containing this tool contains your login information if the tool configuration has values set for API Key ID, or API Key Secret, or if you have logged in using a browser.

The uploaded sample can be shared with QCI users by adding a comma separated list of emails in the Reviewers setting.

Output

The output is a report that shows a summary of the data in the sample, information about the upload, and a link to the sample list in QCI Interpret.