Allele imputation and haplotype determination from databases composed of nuclear families

Abstract

The alleHap package is designed for imputing genetic missing data and\r\nreconstruct nonrecombinant haplotypes from pedigree databases in a\r\ndeterministic way. When genotypes of related individuals are available\r\nin a number of linked genetic markers, the program starts by identifying\r\nhaplotypes compatible with the observed genotypes in those markers\r\nwithout missing values. If haplotypes are identified in parents or\r\noffspring, missing alleles can be imputed in subjects containing missing\r\nvalues. Several scenarios are analyzed: family completely genotyped,\r\nchildren partially genotyped and parents completely genotyped, children\r\nfully genotyped and parents containing entirely or partially missing\r\ngenotypes, and founders and their offspring both only partially\r\ngenotyped. The alleHap package also has a function to simulate pedigrees\r\nincluding all these scenarios. This article describes in detail how our\r\npackage works for the desired applications, including illustrated\r\nexplanations and easily reproducible examples.