Table 1 Performance of different genotypers and de novo callers, measured against 50 bp or longer SV from our LRGT
From: Paragraph: a graph-based structural variant genotyper for short-read sequence data
Type | Deletion | Insertion | ||||||
|---|---|---|---|---|---|---|---|---|
Paragraph | Delly Genotyper | SVTyper (100+ bp) | Manta | Delly | Lumpy (100+ bp) | Paragraph | Manta | |
#Tested TPs | 16,936 | 16,936 | 11,160 | 16,936 | 16,936 | 11,160 | 21,303 | 21,303 |
Recall | 0.84 | 0.76 | 0.70 | 0.62 | 0.61 | 0.64 | 0.88 | 0.35 |
#Tested FPs | 10,778 | 10,778 | 6960 | – | – | – | 11,307 | – |
Precision | 0.92 | 0.85 | 0.98 | – | – | – | 0.89 | – |
F-score | 0.88 | 0.80 | 0.82 | – | – | – | 0.88 | – |