# QC Test Set

## Phenotypes

| # | Phenotype | Type | Contingency | GWAS Result | QC Notes |
|---|-----------|------|-------------|-------------|----------|
| 1 | `morphine__J189` | binary | YES | YES | BŁĄD w usuwaniu (bug in removal) |
| 2 | `morphine__E86` | binary | YES | YES | |
| 3 | `tramadol__L409` | binary | YES | YES | działa zostawianie (retention works) |
| 4 | `zopiclone__M796` | binary | YES | YES | działa usuwanie (removal works) |
| 5 | `simvastatin__prescribed` | binary | needs run | YES | |
| 6 | `warfarin__prescribed` | binary | needs run | YES | |
| 7 | `warfarin__optimal_dose` | continuous | needs run | YES | |
| 8 | `olmesartan__prescribed` | binary | needs run | **NO** | needs GWAS run |
| 9 | `propranolol__prescribed` | binary | needs run | YES | |
| 10 | `p1558_i0__alcohol_intake_freq` | continuous | needs run | YES | |

## GWAS Result Paths (regenie_dosages)

| Phenotype | Result Directory |
|-----------|-----------------|
| morphine__J189 | `result/marpiech_finalregeniedosages_2026_02_27_21_11_14_morphine__J189_regenie_dosages/` |
| morphine__E86 | `result/marpiech_finalregeniedosages_2026_03_04_10_24_45_morphine__E86_regenie_dosages/` |
| tramadol__L409 | `result/marpiech_tramadol_2026_02_04_20_46_26_tramadol__L409_regenie_dosages/` |
| zopiclone__M796 | `result/marpiech_finalregeniedosages_2026_02_28_02_50_52_zopiclone__M796_regenie_dosages/` |
| simvastatin__prescribed | `result/marpiech_finalregeniedosages_2026_02_15_04_42_11_simvastatin__prescribed_regenie_dosages/` |
| warfarin__prescribed | `result/marpiech_finalregeniedosages_2026_02_27_20_08_41_warfarin__prescribed_regenie_dosages/` |
| warfarin__optimal_dose | `result/marpiech_finalregeniedosages_2026_02_15_17_58_25_warfarin__optimal_dose_regenie_dosages/` |
| olmesartan__prescribed | — |
| propranolol__prescribed | `result/marpiech_finalregeniedosages_2026_02_14_20_52_51_propranolol__prescribed_regenie_dosages/` |
| p1558_i0__alcohol_intake_freq | `result/marpiech_finalregeniedosages_2026_02_18_05_14_42_p1558_i0__alcohol_intake_freq_regenie_dosages/` |

## Contingency TSVs

Existing:
- `contingency_morphine__J189.tsv`
- `contingency_morphine__E86.tsv`
- `contingency_tramadol__L409.tsv`
- `contingency_zopiclone__M796.tsv`

Needs run:
- `run_contingency.sh simvastatin__prescribed`
- `run_contingency.sh warfarin__prescribed`
- `run_contingency.sh warfarin__optimal_dose --phenotype-type continuous`
- `run_contingency.sh olmesartan__prescribed` (also needs GWAS)
- `run_contingency.sh propranolol__prescribed`
- `run_contingency.sh p1558_i0__alcohol_intake_freq --phenotype-type continuous`

## QC Plots

Manhattan plots for all phenotypes with GWAS results are in `qc_test/`.