The Filter Somatic Variants (WES) ready-to-use workflow accepts variant tracks () (e.g. the output from the Identify Variants ready-to-use workflow) as input. In cases with heterozygous variants, the reference allele is 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).
- How to run the Filter Somatic Variants (WES) workflow
- Output from the Filter Somatic Variants (WES) workflow