Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads.

ABSTRACT:

Motivation

Hidden Markov model, based on Li and Stephens model that takes into account chromosome sharing of multiple individuals, results in mainstream haplotype phasing algorithms for genotyping arrays and next-generation sequencing (NGS) data. However, existing methods based on this model assume that the allele count data are independently observed at individual sites and do not consider haplotype informative reads, i.e. reads that cover multiple heterozygous sites, which carry useful haplotype information. In our previous work, we developed a new hidden Markov model to incorporate a two-site joint emission term that captures the haplotype information across two adjacent sites. Although our model improves the accuracy of genotype calling and haplotype phasing, haplotype informat

SUBMITTER: Zhang K 

PROVIDER: S-EPMC3777110 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature