Prepare QCI Interpret Upload
The Prepare QCI Interpret Upload tool prepares a sample from several types of tracks and reports that can be uploaded to QCI Interpret or QCI Interpret Translational at a later time with Upload Prepared QCI Interpret Report.
This tool can be used in workflows to select all relevant tracks and reports. It sets name based on input or other metadata and outputs a single report that is ready to be uploaded to QCI Interpret. This is convenient because users won't have to choose multiple track inputs for every workflow output they want to upload to QCI Interpret.
To run the tool, go to:
Tools | Biomedical Genomics Analysis (
) | IPA and QCI Interpret Upload (
) | QCI Interpret Upload (
) | Prepare QCI Interpret Upload (
)
In the first wizard step, select the elements containing the variants that should be uploaded. 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.
In the next step, specify information that should be displayed in QCI Interpret. Under Names, 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 Configuring Workflow Output and Export elements for details.
- Sample name The name of the uploaded sample that will be shown in QCI Interpret.
- Subject ID Set the subject ID of the uploaded sample, leave empty, or use metadata if running as part of a workflow.
- Project Set the project of the uploaded sample, leave empty or use metadata if running as part of a workflow.
Under Elements, specify the reference sequence, reports containing oncology scores that should be included in the upload, reports containing tumor purity values, 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 Calculate TMB Score. The algo must have been set up to detect a TMB status.
- MSI report Include microsatellite instability score and status by including a report output from Detect MSI Status.
- HRD report Include homologous recombination deficiency score and status by including a report output from Calculate HRD Score.
- Tumor purity report Include tumor purity value by including a report from Detect Regional Ploidy.
- Upload reports Include any report. Specified reports will be shown as PDFs in QCI Interpret.
The next step defines how the uploaded VCF will be created. The Prefill VCF setting 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. For details about VCF export settings, see Export in VCF Format.
Output
The output is a report that shows a summary of the data in the sample.