Table 11 Root mean squared error (RMSE) between true and estimated repeat numbers with allelotype using the original BAM file of 10 × and those realigned with STR-realigner, ReviSTER, GATK IndelRealigner, and allelotype with --realign option 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 | --realign option | Original BAM |
|---|---|---|---|---|---|---|
1 | 5345 | 2.477 | 2.695 | 6.017 | 6.009 | 6.009 |
2 | 1160 | 3.545 | 3.740 | 6.948 | 6.885 | 6.899 |
3 | 517 | 3.566 | 3.728 | 6.898 | 6.843 | 6.843 |
4 | 1433 | 3.754 | 3.818 | 7.476 | 7.417 | 7.431 |
5 | 668 | 3.910 | 4.469 | 8.760 | 8.762 | 8.762 |
6 | 472 | 4.319 | 4.265 | 8.232 | 8.217 | 8.233 |
Total | 9595 | 3.116 | 3.309 | 6.752 | 6.727 | 6.732 |