Last update: 20241217
Design statistical genomics v1
Protocol name: design_statistical_genomics_v1
Statistical genomics to find new cohort-level associations with disease. This documention is an incomplete placeholder. This protocol is made up of several steps which together make the joint analysis. Pages on individual methods include VSAT, setID, ACAT, GWAS.
This set of analysis use Design DNA SNV INDEL v1 followed by QV SNV INDEL v1 as input. The following aims are then used to reach the joint analysis.
Aims
| Phase | Aim | Status | Task |
|---|---|---|---|
| Phase 2 | (0) | Complete | QC, PCA, clinical covariates, outcomes |
| Phase 2 | (1) | 2 experiment complete in progress | Single variant association test (SVAT) GWAS |
| Phase 2 | (2) | 2 experiment complete in progress | Variant set association test (VSAT) gene-level |
| Phase 2 | (3) | Complete | ProteoMCLusteR to generate pathway setID |
| Phase 2 | (4) | 1 experiment complete in progress | Variant set association test (VSAT) pathway-level |
| Phase 2 | (6) | 1 experiment complete in progress | Multiomic ACAT |