Table 8 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 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 | 5.261 | 5.128 | 8.904 | 9.126 |
2 | 1160 | 4.779 | 5.984 | 8.879 | 9.162 |
3 | 517 | 3.441 | 5.409 | 8.629 | 8.880 |
4 | 1433 | 4.466 | 6.724 | 10.060 | 10.195 |
5 | 668 | 4.951 | 7.489 | 11.058 | 11.159 |
6 | 472 | 4.854 | 7.179 | 10.385 | 10.652 |
Total | 9595 | 4.966 | 5.809 | 9.308 | 9.517 |