CONTENTS
1. PRELIMINARY INFORMATION
1.1 - Tutorial objective
1.2 - Tutorial material and case study
1.3 - Experiment design and support
1.4 - Installing and activating VariantSeq and the Server-Side
2. STEP-BY-STEP MODE TUTORIAL
2.1. - Preparing your experiment
2.2 - Quality analysis and preprocessing
- Quality analysis
- Preprocessing
2.3 - Mapping
2.4 - Postprocessing
- AddReplaceGroups
- MarkDuplicates
- Base quality score recalibration (BQSR)
2.1.5 - Variant calling
2.6 - Variant filtering
2.7 - Annotation
3. PIPELINE MODE TUTORIAL
4. BIBLIOGRAPHY