FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model.

ABSTRACT:

Motivation

Fast and accurate genotype imputation is necessary for facilitating gene-mapping studies, especially with the ever increasing numbers of both common and rare variants generated by high-throughput-sequencing experiments. However, most of the existing imputation approaches suffer from either inaccurate results or heavy computational demand.

Results

In this article, aiming to perform fast and accurate genotype-imputation analysis, we propose a novel, fast and yet accurate method to impute diploid genotypes. Specifically, we extend a hidden Markov model that is widely used to describe haplotype structures. But we model hidden states onto single reference haplotypes rather than onto pairs of haplotypes. Consequently the computational complexity is linear to size of ref

SUBMITTER: Zhang L 

PROVIDER: S-EPMC4071209 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature