Exome Sequencing of a Multigenerational Human Pedigree (original) (raw)
Figure 3
Estimated error rates.
Sensitivity of genotype calling based on HCDiff SNPs, AllDiff SNPs, and the proposed coverage-dependent genotype calling approach. A) False negative rates are based on concordance with a subset of 44,513 SNPs that overlapped with genotypes obtained with Illumina 1 M Duo BeadChips. The coverage-dependent variant calling approach that calibrates cut-off rates according to array-based genotypes is the most sensitive method, detecting >96% of SNPs at 5x coverage and >99% of all SNPs at ≥8x coverage. B) False positive rates. HCDiff is the most conservative algorithm, resulting in a smaller false positive rate, while the more relaxed dynamic genotype calling algorithm results in twice as high error rates at lower coverage.