Large scale reconstruction of haplotypes from genotype data
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Efficient rule-based haplotyping algorithms for pedigree data
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Linear reduction method for predictive and informative tag SNP selection
International Journal of Bioinformatics Research and Applications
Highly Scalable Genotype Phasing by Entropy Minimization
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Indexing a dictionary for subset matching queries
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
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Although there exist many phasing methods for unrelated adults or pedigrees, phasing and missing data recovery for data representing family trios is lagging behind. This paper is an attempt to fill this gap by considering the following problem. Given a set of genotypes partitioned into family trios, find for each trio a quartet of parent haplotypes which agree with all three genotypes and recover the SNP values missed in given genotype data. Our contributions include (i) formulating the pure-parsimony trio phasing and the trio missing data recovery problems, (ii) proposing two new greedy and integer linear programming based solution methods, and (iii)extensive experimental validation of proposed methods showing advantage over the previously known methods.