Maximum parsimony xor haplotyping by sparse dictionary selection.

ABSTRACT:

Background

Xor-genotype is a cost-effective alternative to the genotype sequence of an individual. Recent methods developed for haplotype inference have aimed at finding the solution based on xor-genotype data. Given the xor-genotypes of a group of unrelated individuals, it is possible to infer the haplotype pairs for each individual with the aid of a small number of regular genotypes.

Results

We propose a framework of maximum parsimony inference of haplotypes based on the search of a sparse dictionary, and we present a greedy method that can effectively infer the haplotype pairs given a set of xor-genotypes augmented by a small number of regular genotypes. We test the performance of the proposed approach on synthetic data sets with different number of individuals and SNPs,

SUBMITTER: Elmas A 

PROVIDER: S-EPMC3852077 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature