Table 5 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 all the STR regions. The best result is underlined

1

5345

1.104

1.054

4.148

4.181

4.152

2

1160

2.638

2.679

5.454

5.762

5.477

3

517

2.778

2.746

4.818

4.768

4.818

4

1433

2.651

2.631

5.386

5.398

5.406

5

668

2.301

2.114

6.617

6.660

6.617

6

472

3.137

3.178

6.071

5.936

6.094

Total

9595

1.959

1.933

4.861

4.914

4.870