High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium.

ABSTRACT: Short read sequencing of diploid individuals does not permit the direct inference of the sequence on each of the two homologous chromosomes. Although various phasing software packages exist, they were primarily tailored for and tested on human data, which differ from other species in factors that influence phasing, such as SNP density, amounts of linkage disequilibrium (LD) and sample sizes. Despite becoming increasingly popular for other species, the reliability of phasing in non-human data has not been evaluated to a sufficient extent. We scrutinized the phasing accuracy for Drosophila melanogaster, a species with high polymorphism levels and reduced LD relative to humans. We phased two D. melanogaster populations and compared the results to the known haplotypes. The performance increase

SUBMITTER: Bukowicki M 

PROVIDER: S-EPMC4916997 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature