Distinct error rates for reference and nonreference genotypes estimated by pedigree analysis.

ABSTRACT: Errors in genotype calling can have perverse effects on genetic analyses, confounding association studies, and obscuring rare variants. Analyses now routinely incorporate error rates to control for spurious findings. However, reliable estimates of the error rate can be difficult to obtain because of their variance between studies. Most studies also report only a single estimate of the error rate even though genotypes can be miscalled in more than one way. Here, we report a method for estimating the rates at which different types of genotyping errors occur at biallelic loci using pedigree information. Our method identifies potential genotyping errors by exploiting instances where the haplotypic phase has not been faithfully transmitted. The expected frequency of inconsistent phase depends o

SUBMITTER: Wang RJ 

PROVIDER: S-EPMC8045694 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature