Fast and Accurate Shared Segment Detection and Relatedness Estimation in Un-phased Genetic Data via TRUFFLE.

ABSTRACT: Relationship estimation and segment detection between individuals is an important aspect of disease gene mapping. Existing methods are either tailored for computational efficiency or require phasing to improve accuracy. We developed TRUFFLE, a method that integrates computational techniques and statistical principles for the identification and visualization of identity-by-descent (IBD) segments using un-phased data. By skipping the haplotype phasing step and, instead, relying on a simpler region-based approach, our method is computationally efficient while maintaining inferential accuracy. In addition, an error model corrects for segment break-ups that occur as a consequence of genotyping errors. TRUFFLE can estimate relatedness for 3.1 million pairs from the 1000 Genomes Project data in a

SUBMITTER: Dimitromanolakis A 

PROVIDER: S-EPMC6612710 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature