Identify Somatic Variants from Tumor Normal Pair (TAS)

The Identify Somatic Variants from Tumor Normal Pair (TAS) template workflow can be used to identify potential somatic variants in a tumor sample when you also have a normal/control sample from the same individual.

When running this workflow the reads are mapped and the variants identified. 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 relevant databases like 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.

Before starting the workflow, you will need to import in the CLC Workbench a file with the genomic regions targeted by the amplicon or hybridization kit. Such a file (a BED or GFF file) is usually available from the vendor of the enrichment kit and sequencing machine. Use the Import | Tracks tool to import it in your Navigation Area.


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