A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels.

ABSTRACT:

Background

Haplotype reconstruction (phasing) is an essential step in many applications, including imputation and genomic selection. The best phasing methods rely on both familial and linkage disequilibrium (LD) information. With whole-genome sequence (WGS) data, relatively small samples of reference individuals are generally sequenced due to prohibitive sequencing costs, thus only a limited amount of familial information is available. However, reference individuals have many relatives that have been genotyped (at lower density). The goal of our study was to improve phasing of WGS data by integrating familial information from haplotypes that were obtained from a larger genotyped dataset and to quantify its impact on imputation accuracy.

Results

Aligning a pre-phased WGS pane

SUBMITTER: Faux P 

PROVIDER: S-EPMC5434521 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature