In the CLC Genomics Workbench resequencing is the overall category for applications comparing genetic variation of a sample to a reference sequence. This can be targeted resequencing of a single locus or whole genome sequencing. The overall workflow will typically involve read mapping, some sort of variant detection and interpretation of the variants.
This chapter describes the tools relevant for the resequencing workflows downstream from the actual read mapping which is described in Read mapping.
- Variant filtering
- Variant annotation
- Variants comparison
- Variant quality control
- Functional consequences
- Create Consensus Sequences from Variants