The Somatic Cancer ready-to-use workflows are workflows that have been tailored to cancer research. In this category it is possible to find e.g. workflows that can compare variants in matched tumor normal pairs. The workflows found in the Somatic Cancer category, use the "Low Frequency Variant Detection" for variant calling. The advantages of using this variant caller when analyzing cancer data are that 1) it does not take ploidy into consideration, and 2) it is particularly good at picking up low frequency variants in contrast to the other variant callers.
The workflows that are available in this category are:
- Filter Somatic Variants: Removes variants outside the target region (only targeted experiments) and common variants present in publicly available databases. Annotates with gene names, conservation scores, and information from relevant databases.
- Identify Somatic Variants from Tumor Normal Pair: Removes germline variants by referring to the control sample read mapping, removes variants outside the target region (in case of a targeted experiment), and annotates with gene names, conservation scores, amino acid changes, and information from relevant databases.
- Identify Variants: Calls variants in the mapped and locally realigned reads, removes false positives and, in case of a targeted experiment, removes variants outside the targeted region. Variant calling is performed with the Low Frequency Variant Detection tool.