Phasing and Missing Data Recovery in Family Trios
نویسندگان
چکیده
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.
منابع مشابه
Family trio phasing and missing data recovery
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/offspring haplotypes explaining each trio without recombi...
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Description Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent tr...
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