Upload to QCI Interpret
The Upload to QCI Interpret tool can upload variants as well as TMB and MSI scores to QCI Interpret or QCI Interpret Translational. To facilitate the upload, variant tracks are first exported to VCF and then uploaded using provided login details.
To run the tool, go to:
Tools | Biomedical Genomics Analysis (
) | IPA and QCI Interpret Upload (
) | QCI Interpret Upload (
) | Upload to QCI Interpret (
)
In the first wizard step, select the elements containing the variants that should be uploaded (see figure 9.2). Supported input elements are:
- Variant track(s) Add variant tracks to include variants in the upload. If multiple variant tracks are selected, all variants in the variant tracks are uploaded except duplicate variants, where only the variant with the highest quality is included.
- CNV track Add a CNV track to include copy number variations.
- Fusion track Add a fusion track to include fusions.
- Inversion track Add an inversion track to include inversions.
Figure 9.1: Select the elements containing variants, CNVs, fusions and inversions that should be uploaded.
In the next step, specify information that should be displayed in QCI Interpret (see figure 9.3). Under Name, if a field is left empty, the name of the first selected element is used as the sample name. It is possible to use metadata to define the sample name if the tool is run as part of a workflow (see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Configuring_Workflow_Output_Export_elements.html).
- Sample name The name of the uploaded sample that will be shown in QCI Interpret.
- Subject ID The subject ID of the uploaded sample that will be shown in QCI Interpret.
- Project The project of the uploaded sample that will be shown in QCI Interpret.
Under Elements, specify the reference sequence, reports containing oncology scores that should be included in the upload and add any reports that should be available as PDFs in QCI Interpret:
- Reference sequence track To generate the VCF the tool needs a reference track. Hg19 and hg38 references are supported.
- TMB report Include tumor mutation burden value and status by including a report output from the Calculate TMB Score tool in the Biomedical Genomics Analysis plugin. The algo must have been set up to detect a TMB status.
- MSI report Include microsatellite instability status by including a report output from the Detect MSI Status tool in the Biomedical Genomics Analysis plugin.
- Upload reports Include any report. Specified reports will be shown as PDFs in QCI Interpret.
Figure 9.2: Provide information that should be shown in QCI Interpret, the reference sequence for the uploaded variants, oncology scores and any reports that should be available as PDFs in QCI Interpret.
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 https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Export_in_VCF_format.html.
Figure 9.3: Choosing QCI region and log in.
In the final step choose your QCI Region and how to log in. See figure 9.4. 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.
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.