Table 1. Sanger validation of SNVs, short indels and de novo variants.
| Variant class | FDR | Sites |
|---|---|---|
| GATK-SNVs | ||
| Overall | 0.02 | 46 |
| Novel | 0.05 | 21 |
| Loss of function | 0.00 | 25 |
| GATK-indels | ||
| Overall | 0.15 | 26 |
| Repeat | 0.27 | 15 |
| Non-repeat | 0.00 | 11 |
| Novel | 0.18 | 11 |
| Loss of function | 0.13 | 15 |
| De novo variants | ||
| SNVs | 0.04 | 24 |
| Indels | 0.11 | 19 |
FDR, false discovery rate; GATK, Genome Analysis Toolkit; SNV, single nucleotide variation.
Sanger sequencing experiments were used to assay the FDR for 21 novel, 25 loss of function and 24 de novo SNVs. For indels a total of 11 novel, 15 loss of function and 19 de novo indels were assayed.