Table 12 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 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 | 5304 | 2.413 | 2.656 | 5.740 | 5.732 | 5.732 |
2 | 1128 | 3.336 | 3.420 | 6.440 | 6.371 | 6.386 |
3 | 505 | 3.057 | 3.090 | 6.456 | 6.396 | 6.396 |
4 | 1394 | 3.398 | 3.479 | 7.045 | 6.980 | 6.995 |
5 | 647 | 3.766 | 4.199 | 8.015 | 8.017 | 8.017 |
6 | 462 | 3.688 | 3.872 | 7.907 | 7.892 | 7.909 |
Total | 9440 | 2.906 | 3.099 | 6.363 | 6.336 | 6.341 |