Resequencing analysis tools
In the Biomedical 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.
Subsections
- Map Reads to Reference
- Mapping output
- Summary mapping report
- Mapping SOLid reads in color space
- Local realignment
- Merge mapping results
- Remove duplicate mapped reads
- Trim primers of mapped reads
- Extract reads based on overlap
- InDels and Structural Variants
- Copy Number Variant Detection
- Coverage analysis
- Variant Detectors - overview
- Fixed Ploidy Variant Detection
- Low Frequency Variant Detection
- Basic Variant Detection
- Variant Detectors - error model estimation
- Variant Detectors - filters
- Variant Detectors - the outputs
- The Fixed Ploidy and Low Frequency variant callers: detailed descriptions
- Variant data
- Detailed information about overlapping paired reads
- Identify Known Mutations from Sample Mappings