Table 9 Root mean squared error (RMSE) between true and estimated repeat numbers with RepeatSeq using the original BAM file of 10 × and those realigned with STR-realigner, ReviSTER, and GATK IndelRealigner for commonly called 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 | 4505 | 5.461 | 5.363 | 9.047 | 9.184 |
2 | 860 | 4.878 | 6.307 | 9.238 | 9.436 |
3 | 396 | 3.531 | 4.862 | 8.520 | 8.817 |
4 | 1023 | 4.449 | 5.954 | 9.828 | 9.899 |
5 | 497 | 5.188 | 6.835 | 10.504 | 10.638 |
6 | 371 | 4.622 | 6.771 | 10.451 | 10.773 |
Total | 7652 | 5.129 | 5.712 | 9.323 | 9.474 |