Chunk #34 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Detecting genotyping error
We can also use this model to detect genotyping error at locus , by summing over the posterior probabilities of inheritance states that have inconsistent haplotypes. We use the indicator variable to denote the absence/presence of a genotyping error at locus in a duo. Then we havewhere is the posterior probability of inheritance pattern and can be efficiently calculated from the HMM model. This is the probability of a genotyping error occurring in at least one member of the duo given the observed haplotypes. We show on simulated and real data that masking genotypes with yields a drop in switch error rates suggesting that this is an effective error detection method.
