Analyze Tumor Normal Pair
The Analyze Tumor Normal Pair template workflow is designed to identify potential somatic variants from matched tumor and normal samples from the same individual.
The workflow supports analysis of variant calls from multiple data types, including:
- QIAseq panel data.
- Whole-genome sequencing (WGS) data.
- Whole-exome sequencing (WES) data.
- Targeted amplicon sequencing (TAS) data.
- RNA-Seq data.
The workflow takes as input a variant track from both the tumor and the normal sample and, optionally, read mappings and target regions can also be supplied to refine the analysis. When read mappings and target regions are supplied, the workflow annotates variants that are located in low-coverage regions within the normal sample. Such variants may not be reliably detected in the normal sample, and could therefore be germline variants even though they appear somatic.
Note! To ensure accurate identification of somatic variants, it is essential that both the tumor and normal samples meet the following criteria:
- Consistent experimental methodology. The data must be generated using the same sequencing approach and experimental protocol.
- Uniform bioinformatics processing. Read mapping and variant calling for both samples must be performed using the same workflow, parameters, and filtering cutoffs.
Launching the workflow
To run this workflow, go to:
Workflows | Template Workflows | Biomedical Workflows (
) | Comparative Analysis (
) | Analyze Tumor Normal Pair (
)
Options can be configured in the following dialogs:
- Choose where to run. If you are connected to a CLC Server via the CLC Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
- Specify workflow path. The following paths can be configured:
- Use read mappings. Specify whether you will provide tumor/normal read mappings. This will enable analysis of low-coverage regions and will add QC for Read Mapping sections to the sample/combined reports.
- Identify low coverage targets. Specify whether you will provide a target region track. In combination with the read mappings, this will extend the analysis with low-coverage regions in tumor and normal samples and a comparison of target region coverage in the combined report.
- Select tumor/normal variant track. Select variant tracks for tumor and normal samples. Variants should be detected using the same workflow for both samples.
- Select tumor/normal read mapping, if "Use read mappings" is enabled in "Specify workflow path". Select read mappings for the tumor and normal samples.
- Select target regions, if "Identify low coverage targets" is enabled in "Specify workflow path". Select target regions matching the samples.
- Specify reference data handling. Select a Reference Data Set matching the genome of the input tracks, see Reference data management for details.
- Configure batching, if running the workflow in batch mode. Define the batch units.
- Batch overview, if running the workflow in batch mode. Verify that the batching is as intended.
- Identify low coverage regions (tumor/normal): Set a coverage cutoff defining low-coverage regions in the tumor and normal samples, respectively. The same cutoff should be used for tumor and normal. Somatic variants will be annotated with regards to whether they are found in a low-coverage region in the normal sample.
- Result handling. Choose if a workflow result metadata and/or log should be saved.
- Save location for new elements. Choose where to save the data, and press Finish to start the analysis.
Subsections