Table 3 Number of indels and Mendelian error rates using Varscan, SAMtools and SeqGene
From: SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
| Â | Â | VarScan | SAMtools | SeqGene | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Father | Mother | Daughter | Father | Mother | Daughter | Father | Mother | Daughter |
| Â | After SNP Filter | 696 | 522 | 522 | 539 | 560 | 634 | 637 | 628 | 703 |
Coverage > 10 | After Family Filter | 356 (4) | 330 (4) | 331 (3) | 279 (5) | 279 (4) | 278 (8) | 320 (4) | 318 (3) | 322 (6) |
| Â | Mendelian Error Rate (%) | 1.1 | 1.2 | 0.9 | 1.8 | 1.4 | 2.9 | 1.2 | 0.9 | 1.9 |
| Â | After SNP Filter | 690 | 503 | 506 | 389 | 355 | 413 | 478 | 416 | 472 |
Coverage > 20 | After Family Filter | 340 (4) | 316 (4) | 319 (3) | 180 (2) | 182 (2) | 178 (1) | 223 (1) | 223 (1) | 223 (1) |
| Â | Mendelian Error Rate (%) | 1.2 | 1.3 | 0.9 | 1.1 | 1.1 | 0.6 | 0.4 | 0.4 | 0.4 |