Filter Somatic Variants (TAS)
If you are analyzing a list of variants that have been detected in a tumor or blood sample where no control sample is available from the same subject, you can use the Filter Somatic Variants (TAS) template workflow to identify potential somatic variants. The purpose of this template workflow is to use publicly available (or your own) databases, with common variants in a population, to extract potential somatic variants whenever no control/normal sample from the same subject is available.
This workflow accepts variant tracks () (e.g. the output from the Identify Variants template workflow) as input. Variants that are identical to the human reference sequence are first filtered away, then variants outside the targeted region are removed, and lastly, variants found in the Common dbSNP, 1000 Genomes Project, and HapMap databases are deleted. Variants in those databases are assumed to not contain relevant somatic variants.
Please note that this tool will likely also remove inherited cancer variants that are present at a low percentage in a population.
Next, the remaining somatic variants are annotated with gene names, amino acid changes, conservation scores and information from ClinVar (known variants with medical impact) and dbSNP (all known variants).