Variant Storage Engine

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
2. Load
3. Annotate
4. 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)

Query filters