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Pedigree-Based Haplotype Reconstruction, Identification of Cross-overs and Detection of Map and Genotyping Errors using PHASEBOOK
Haplotype reconstruction is important in many applications in animal genomics. In livestock species, thanks to the availability of large half-sibs families, phasing methods can rely on strong familial information and results are very accurate. However, most methods are sensitive to genotyping and map errors which will be more common with next generation sequencing data. Such problems are particularly important when studying recombination rate. We herein describe a novel algorithm which is robust to genotyping errors and which can identify errors in marker maps. Using a large dairy cattle data set genotyped with high-density SNP arrays, we show that the novel algorithm strongly reduces the occurrence of spurious cross-overs and identifies map errors for most of the bovine autosomes. Further research will be conducted to characterize the novel method and to fully describe the identified map errors.
Keywords:
Haplotype reconstruction, Recombination, Map errors
