Article
SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium.
Genetics, selection, evolution : GSE - 26 Jun 2018
Calus Mario P L, Vandenplas Jérémie
Abstract excerpt
BACKGROUND: High levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, this warrants pruning of genotyping data for high LD. We developed an algorithm, named SNPrune, which enables the rapid detection of any pair of SNPs in complete or high LD throughout the genome....
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