The "Identify Somatic Variants from Tumor Normal Pair" ready-to-use workflow can be used to identify potential somatic variants in a tumor sample when you also have a normal/control sample from the same patient.
When running the "Identify Somatic Variants from Tumor Normal Pair" the reads are mapped and the variants identified. An internal workflow removes germline variants that are found in the mapped reads of the normal/control sample and variants outside the target region are removed as they are likely to be false positives due to non-specific mapping of sequencing reads. Next, remaining variants are annotated with gene names, amino acid changes, conservation scores and information from clinically relevant databases like COSMIC (known cancer associated variants) and ClinVar (variants with clinically relevant association). Finally, information from dbSNP is added to see which of the detected variants have been observed before and which are completely new.
- Import your targeted regions
- How to run the "Identify Somatic Variants from Tumor Normal Pair" ready-to-use workflow