Abstract
Background Haplotype inference is an essential stage in genetic linkage analysis and estimation methods are also very frequently used to reconstruct haplotypes in current genetic association studies. Most of the latter are focused on haplotype phasing from recombinant DNA areas of unrelated individuals and use likelihood-based methods to infer the presence of alleles in several loci with very time-consuming probabilistic algorithms. So far, literature does not analyze haplotypes using deterministic techniques, and there are hardly any alternative methods for constructing haplotypes from non-recombinant DNA areas, despite the fact that computational inference by probabilistic models may cause a large number of incorrect inferences.
Highlights
Haplotype inference is an essential stage in genetic linkage analysis and estimation methods are very frequently used to reconstruct haplotypes in current genetic association studies
Description and results We have developed an algorithm called alleHap, which is able to impute alleles from parent-offspring pedigree databases with missing family members, to later construct their corresponding, unambiguous haplotypes
The alleHap algorithm is based on a preliminary analysis of all possible combinations that may exist in the genotyping of a family, considering that each member, Table 1 Possible allelic combinations in a parent-offspring pedigree
Summary
Haplotype inference is an essential stage in genetic linkage analysis and estimation methods are very frequently used to reconstruct haplotypes in current genetic association studies. Description and results We have developed an algorithm called alleHap, which is able to impute alleles from parent-offspring pedigree databases with missing family members, to later construct their corresponding, unambiguous haplotypes.
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