NDLI: Haplotype reconstruction from SNP alignment

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Haplotype reconstruction from SNP alignment

Content Provider	ACM Digital Library
Author	Kim, Jong Hyun Li, Lei Waterman, Michael S.
Abstract	In this paper we describe a method for statistical reconstruction of haplotypes from a set of aligned SNP fragments. We consider the case of a pair of homologous human chromosomes, one from the mother and the other from the father. After fragment assembly and SNP detection, we wish to reconstruct the two haplotypes of the parents. Given a set of SNP sites inferred from the assembly alignment, we wish to divide the fragment set into two subsets, each of which represents one chromosome. Our method is based on a statistical model of sequencing errors, compositional information and haplotype memberships.We calculate probabilities of different haplotypes conditional on the alignment. Due to computational complexity, we first determine phases for neighboring SNPs. Then we connect them and construct haplotype segments. Also we compute the accuracy or confidence of the reconstructed haplotypes. We discuss other issues such as alternative methods, parameter estimation, computational efficiency, and relaxation of assumptions.
Starting Page	207
Ending Page	216
Page Count	10
File Format	PDF
ISBN	1581136358
DOI	10.1145/640075.640102
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2003-04-10
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Alignment Snp Confidence Genotype Haplotype Shotgun sequencing
Content Type	Text
Resource Type	Article

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