Overview
- Study oriented
- Cohort definition
Different vcf types: Aggregated VCFs Variant files with no sample specific values. Just aggregated data Merged VCFs Variant files with a batch of samples with specific samples data. * gVCFs Single sample files with information for all the positions.
Index Pipeline
Split into steps: 1. Transform 1. Load 1. Annotate 1. Calculate Stats
1) Transform
- Validation
- [[Variant Normalization]]
2) Load
- Variant Merging Plugin dependent.
3) Variant Annotation
Annotate variants using CellBase annotator. Can use other annotators like VEP.
4) Variant Stats
- Variant stats (cohorts)
- Global stats
- Sample stats (pending)