Table 2 Root mean squared error (RMSE) between true and estimated repeat numbers with RepeatSeq using the original BAM file of 40 × and those realigned with STR-realigner, ReviSTER, and GATK IndelRealigner for all the STR regions. The best result is underlined
From: STR-realigner: a realignment method for short tandem repeat regions
Period | No. of regions | STR-realigner | ReviSTER | IndelRealigner | Original BAM |
|---|---|---|---|---|---|
1 | 5345 | 3.726 | 2.700 | 8.273 | 8.461 |
2 | 1160 | 2.648 | 4.648 | 8.213 | 8.539 |
3 | 517 | 2.151 | 4.022 | 8.242 | 8.601 |
4 | 1433 | 3.199 | 5.726 | 9.523 | 9.597 |
5 | 668 | 3.885 | 6.701 | 10.156 | 10.325 |
6 | 472 | 2.431 | 5.976 | 10.185 | 10.437 |
Total | 9595 | 3.421 | 4.162 | 8.705 | 8.900 |