Table 3 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 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 | 4659 | 3.858 | 2.718 | 8.694 | 8.891 |
2 | 900 | 2.471 | 4.815 | 8.735 | 9.084 |
3 | 410 | 2.402 | 3.265 | 8.548 | 8.930 |
4 | 1084 | 3.152 | 4.428 | 9.688 | 9.796 |
5 | 536 | 3.600 | 5.855 | 10.219 | 10.422 |
6 | 399 | 2.248 | 5.593 | 10.498 | 10.793 |
Total | 7988 | 3.484 | 3.741 | 9.038 | 9.253 |