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 Prepare QCI Interpret Upload, go to:
Toolbox | Biomedical Genomics Analysis () | QCI Interpret Integration () | Prepare QCI Interpret Upload ()
In the tool wizard, choose which elements to upload.
The first step defines inputs. Supported input elements are:
- Variant track(s) Add variant tracks to include variants. Choosing multiple variant tracks exports all variants in the variant tracks, for duplicates only the variant with the highest quality is exported.
- 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.
The next step is to define how the QCI Interpret sample will look in QCI:
- Sample name The name of the uploaded sample shown in QCI Interpret. Leaving it empty will use a name of a element. Use metadata if running as part of a workflow (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Configuring_input_output_elements.html)
- Subject ID Set the subject ID, leave empty, or use metadata if running as part of a workflow.
- Project Set the project, leave empty or use metadata if running as part of a workflow.
The next step defines a reference and extra values that can be added to the sample:
- 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 these reports as PDF in the sample uploaded to 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 http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Export_in_VCF_format.html.
The output is a report that shows a summary of the data in the sample.