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, go to:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_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 defines inputs. Supported input elements are:

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

The next step defines a reference and extra values that can be added to 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 9.1: Choosing QCI region and log in.

In the final step choose your QCI Region and how to log in. See figure 9.1. 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 CLC 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 bioinformaticslicense@qiagen.com and ask for confirmation if the QCI account is API-enabled. The license team can then provide the link to API Explorer page where you can log in to see the API key ID and 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.


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.