Table 1.
Quick reference for definitions of variant categories defined and used frequently throughout this study
| Variant categories | Other names | Definition |
|---|---|---|
| Common ground truth | WGS variants | Variants derived from WGS |
| Pooled read | Variants derived from pooled-read bulk calling on single-cell sequencing | |
| Individual-cell variants | Variants derived from individual-cell calling on single-cell sequencing | |
| Pooled true positive | TP | Pooled-read variant that has a matching WGS variant |
| Pooled false negative | FN | WGS variant not detected in pooled-read variant calling on single-cell sequencing |
| Rare positive | RP | Variant that was detected in single-cell sequencing that was not present in the common ground-truth set |
| Union of rare positive (URP) | scRNA-RP/scATAC-RP | Union of rare positive variant calls for all callers performed on pooled scRNA-seq or scATAC-seq reads |
| Multimodal rare positive | MRP | URP variants seen in both scATAC-seq and scRNA-seq modalities |
| Single-cell-unique (scu) | scRNA-scu/scATAC-scu | Variant detected at the single-cell level in single-cell sequencing that was not called on pooled reads nor found in WGS |
