Benchmarking phasing software with a whole-genome sequenced cattle pedigree.

ABSTRACT:

Background

Accurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are available but their accuracy must be evaluated for samples with different properties (population structure, marker density, etc.). We herein took advantage of whole-genome sequence data available for a Holstein cattle pedigree containing 264 individuals, including 98 trios, to evaluate several population-based phasing methods. This data represents a typical example of a livestock population, with low effective population size, high levels of relatedness and long-range linkage disequilibrium.

Results

After stringent filtering of our sequence data, we evaluated several population-based phasing programs including one or more versio

SUBMITTER: Oget-Ebrad C 

PROVIDER: S-EPMC8845340 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature