Table 3.
Mendelian concordance of SV genotyping methods on trio datasets
| SV genotyping method | MCR | ||
|---|---|---|---|
| HG002 Tier 1 | HG002 Tier 2 | HG005 | |
| cuteSV | 0.92 | 0.83 | 0.95 |
| LRcaller | 0.98 | 0.96 | 0.98 |
| Sniffles | 0.91 | 0.92 | 0.94 |
| SVJedi | 0.97 | 0.96 | 0.97 |
| VaPoR | 0.95 | 0.92 | 0.96 |
The Ashkenazim trio includes son HG002, father HG003, and mother HG004. The Chinese trio includes son HG005, father HG006, and mother HG007. Performance was estimated based on ~ 30× PacBio CLR data. The alignment files were from minimap2 because its output was compatible with all SV genotyping methods
MCR Mendelian concordance rate