Table 2 Number of SNPs 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 | 26458 | 19814 | 20788 | 39657 | 24384 | 26971 | 23522 | 22776 | 24097 |
Coverage > 10 | After Family Filter | 16037 (235) | 14392 (145) | 15048 (194) | 15775 (375) | 13174 (324) | 13556 (458) | 15678 (131) | 15541 (128) | 15809 (191) |
| Â | Mendelian Error Rate (%) | 1.5 | 1.0 | 1.3 | 2.3 | 2.4 | 3.6 | 0.8 | 0.8 | 1.2 |
| Â | After SNP Filter | 23444 | 16317 | 17639 | 27814 | 15797 | 18060 | 18805 | 16354 | 17889 |
Coverage > 20 | After Family Filter | 13992 (124) | 12594 (93) | 13244 (147) | 9745 (90) | 8522 (93) | 8674 (140) | 12001 (63) | 11887 (53) | 12202 (89) |
| Â | Mendelian Error Rate (%) | 0.9 | 0.7 | 1.1 | 0.9 | 1.1 | 1.6 | 0.5 | 0.4 | 0.7 |