Data from: Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. In The Center for GWAS in Outbred Rats Database (C-GORD)

All relevant tools and software used to generate the data in this object are noted below and in the Methods section of the associated publication.
GWAS: GEMMA v0.97
Converting genotype probabilities into dosages: QCTOOL v2
Converting genotype probabilities into Hard-Called Genotypes: PLINK v2.0
LD pruning of the genotype data : PLINK v1.90
Command used to LD-prune the genotype data in PLINK v1.90 : --indep-pairwise 50 5 0.95
The 50 is the number of variants to look at in a window, the 5 is the number of variants to shift the windows side way each step, and the 0.95 is the r2 threshold for trimming SNPs.