Table 6 Root mean squared error (RMSE) between true and estimated repeat numbers with allelotype using the original BAM file of 40 × and those realigned with STR-realigner, ReviSTER, GATK IndelRealigner, and allelotype with --realign option 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 | --realign option | Original BAM |
|---|---|---|---|---|---|---|
1 | 5333 | 1.009 | 0.955 | 4.024 | 4.058 | 4.028 |
2 | 1141 | 2.475 | 2.489 | 5.086 | 5.420 | 5.111 |
3 | 511 | 2.472 | 2.435 | 4.490 | 4.435 | 4.490 |
4 | 1414 | 2.270 | 2.371 | 5.157 | 5.152 | 5.177 |
5 | 661 | 2.058 | 1.865 | 6.263 | 6.308 | 6.263 |
6 | 467 | 2.476 | 2.977 | 5.888 | 5.747 | 5.912 |
Total | 9527 | 1.729 | 1.755 | 4.649 | 4.702 | 4.659 |