Methods of tagSNP selection and other variables affecting imputation accuracy in swine.

ABSTRACT:

Background

Genotype imputation is a cost efficient alternative to use of high density genotypes for implementing genomic selection. The objective of this study was to investigate variables affecting imputation accuracy from low density tagSNP (average distance between tagSNP from 100kb to 1Mb) sets in swine, selected using LD information, physical location, or accuracy for genotype imputation. We compared results of imputation accuracy based on several sets of low density tagSNP of varying densities and selected using three different methods. In addition, we assessed the effect of varying size and composition of the reference panel of haplotypes used for imputation.

Results

TagSNP density of at least 1 tagSNP per 340kb (~7000 tagSNP) selected using pairwise LD information wa

SUBMITTER: Badke YM 

PROVIDER: S-EPMC3734000 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature