How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species.

ABSTRACT:

Background

PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and pet species are used to demonstrate the importance of PLINK input settings. Moreo

SUBMITTER: Meyermans R 

PROVIDER: S-EPMC6990544 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature