Phasing and missing data recovery in family trios

Abstract

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. © Springer-Verlag Berlin Heidelberg 2005.