Estimates haplotypes in filial-1 (F1) -populations by using short DNA sequence reads and parent-offspring relationships. PopPoly exploits the family information to enhance variant dosage estimation of haplotypes of the tuberisation and maturity loci in the population at the detected single-nucleotide polymorphism (SNP) sites. This algorithm assumes that all the population haplotypes must be present in the parents. It also employs the pedigree information to identify and adjust wrongly estimated SNP dosages.
Bioinformatics Group, Wageningen UR, The Netherlands; Wageningen UR Plant Breeding, The Netherlands
PopPoly funding source(s)
Supported by the graduate school Experimental Plant Sciences (EPS) of the Wageningen University and Research and by the project initiative “Novel genetic and genomic tools for polyploid crops” (project number BO-26.03-009-004).
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