Add VEPQA ClinVar SFT v0 dataset

README.md

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+---
+configs:
+- config_name: binary
+  data_files:
+  - split: train
+    path: binary/train-*
+- config_name: clinvar_levels
+  data_files:
+  - split: train
+    path: clinvar_levels/train-*
+- config_name: pathogenic_pairwise
+  data_files:
+  - split: train
+    path: pathogenic_pairwise/train-*
+- config_name: all_tasks
+  data_files:
+  - split: train
+    path: all_tasks/train-*
+---
+
+# VEPQA
+
+Multi-config VEP SFT prototype built from raw ClinVar `variant_summary.txt.gz`
+and UCSC hg38 sequence windows.
+
+Configs:
+
+- `binary`: binary benign/likely benign vs pathogenic/likely pathogenic classification.
+- `clinvar_levels`: finer-grained ClinVar label classification over the retained benign/pathogenic levels.
+- `pathogenic_pairwise`: reference-vs-alternate sequence preference for pathogenic/likely pathogenic variants.
+- `all_tasks`: concatenation of the above configs for quick smoke tests.
+
+Row format:
+
+- `question` / `prompt`: user-facing prompt.
+- `answer` / `gold_answer_json`: deterministic gold JSON target.
+- `messages`: two-turn SFT messages list.
+- `choices`: allowed answer labels for the task.
+- audit metadata: ClinVar IDs, genomic position, review status, sequence hashes, and benchmark exclusion status.
+
+Counts:
+
+```json
+{
+  "all_tasks": 180,
+  "binary": 80,
+  "clinvar_levels": 80,
+  "pathogenic_pairwise": 20
+}
+```
+
+Label counts by task:
+
+```json
+{
+  "binary": {
+    "Benign": 23,
+    "Benign/Likely benign": 8,
+    "Likely benign": 9,
+    "Likely pathogenic": 3,
+    "Pathogenic": 19,
+    "Pathogenic/Likely pathogenic": 18
+  },
+  "clinvar_levels": {
+    "Benign": 23,
+    "Benign/Likely benign": 8,
+    "Likely benign": 9,
+    "Likely pathogenic": 3,
+    "Pathogenic": 19,
+    "Pathogenic/Likely pathogenic": 18
+  },
+  "pathogenic_pairwise": {
+    "Likely pathogenic": 2,
+    "Pathogenic": 12,
+    "Pathogenic/Likely pathogenic": 6
+  }
+}
+```
+
+Notes:
+
+- The binary task uses pathogenic/likely pathogenic terminology, not malignant terminology.
+- Confidence/evidence strength is intentionally not a target because review-status metadata is not provided to the model in the prompt.
+- Carbon eval overlap was checked before sampling; BRCA2 hg19-vs-GRCh38 liftover remains a noted follow-up caveat in the project plan.
+- Existing Claude-generated SFT data and DataForge/Gemma rollouts are not used.