Figure 1: QQ plots for type I error rate simulation studies (gTDT results) with different scenarios of error patterns.
From: The impact of genotype calling errors on family-based studies
We considered four scenarios to mimic this error pattern: 1. r2 (the error rate of calling homozygote 0/0 as heterozygote 0/1) = 0; r1 (the error rate of calling heterozygote 0/1 as homozygote 0/0) = 1%, 5% or 10% in parents; 2. r2 = 0; r1 = 1%, 5% or 10% in offspring; 3. r1 = 0; r2 = 0.1%, 0.5% or 1% in parents; 4. r1 = 0; r2 = 0.1%, 0.5% or 1% in offspring. The 95% point-wise confidence band (gray area) is computed under the assumption of the p-values being drawn independently from a uniform [0, 1] distribution.
