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.
First comes a description of a tool to perform quality check of targeted resequencing approaches, next we describe the three variant callers that come with the CLC Genomics Workbench for finding variants, followed by a section describing a coverage analysis tool used to identify fluctuations in coverage. Next, the format of the variants are described, and finally we go through the various tools for filtering, comparing and annotating variants.
- Create Statistics for Target Regions
- Variant Detectors - overview
- Basic Variant Detection
- Fixed Ploidy Variant Detection
- Low Frequency Variant Detection
- Variant Detectors - error model estimation
- Variant Detectors - filters
- Variant Detectors - the outputs
- The Fixed Ploidy and Low Frequency variant callers: detailed descriptions
- InDels and Structural Variants
- Variant data
- Detailed information about overlapping paired reads
- Annotate and filter variants
- Comparing variants
- Predicting functional consequences