Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats.

ABSTRACT: The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have als

SUBMITTER: Gileta AF 

PROVIDER: S-EPMC7341140 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature