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 work flow will typically involve read mapping, some sort of variant detection and interpretation of the variants.

This chapter describes the tools relevant for the resequencing work flows downstream from the actual read mapping which is described in Read mapping.

First comes a description of a tool to perform quality check of targeted resequencing approaches, next we describe the two variant callers that come with the CLC Genomics Workbench for finding small variants (there is a plug-in for identifying structural variants available in beta). Next, the format of the variants are described, and finally we go through the various tools for filtering, comparing and annotating variants.