Table 2. Comparison of GINDEL, two versions of Genome STRiP (with different setting of the effective length threshold), Pindel and Clever-sv on simulated data.
Coverage | Length | Del. Num. | GINDEL | Genome STRiP v1 | Genome STRiP v2 | Pindel | Clever-sv |
10× | 50–200 | 70 | 0.9869 | 0.0000 | 0.6254 | 0.5476 | 0.9857 |
200–400 | 46 | 0.9769 | 0.4423 | 0.8349 | 0.5502 | 0.9859 | |
400–500 | 13 | 1.0000 | 0.8516 | 0.9327 | 0.3333 | 1.0000 | |
500–1500 | 34 | 1.0000 | 0.9942 | 0.9942 | 0.5830 | 0.9948 | |
>1500 | 58 | 0.9979 | 0.9805 | 0.9805 | 0.5950 | 0.9540 | |
6.4× | 50–200 | 70 | 0.9791 | 0.0000 | 0.5679 | - | 0.8867 |
200–400 | 46 | 0.9697 | 0.3927 | 0.7869 | - | 0.9754 | |
400–500 | 13 | 1.0000 | 0.8496 | 0.9162 | - | 0.9915 | |
500–1500 | 34 | 1.0000 | 0.9542 | 0.9542 | - | 0.9699 | |
>1500 | 58 | 0.9967 | 0.9548 | 0.9667 | - | 0.9345 | |
4.2× | 50–200 | 70 | 0.9645 | 0.0000 | 0.4429 | - | 0.6756 |
200–400 | 46 | 0.9651 | 0.3562 | 0.6984 | - | 0.9068 | |
400–500 | 13 | 1.0000 | 0.8308 | 0.8940 | - | 0.9538 | |
500–1500 | 34 | 0.9979 | 0.9144 | 0.9144 | - | 0.9458 | |
>1500 | 58 | 0.9963 | 0.9686 | 0.9801 | - | 0.8966 |
Results on the percentage of correctly called genotypes are given for deletions with different lengths. Del. Num. indicates the number of deletions in specific length (the number of genotypes is Del. Num. multiply the number of individuals), and because Pindel discovers 104 out of the 221 deletions, so the number of deletions in each specific length (from small to large) are: 24, 21, 5, 20, and 34 respectively. Pindel does not call genotype for data with lower coverages. So no results are reported.