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Multi-trait_simulations
Simulation program for single and multi-traits based purely on pedigree. Different mating designs (ranging from nested, factorial to random union of gamete), selection criterion (mass, high and low TBV, index selection), genetic and residual correlations have been implementeddEBV_Garrick
Deregression based on Garrick et al. (2009). With pedigree and files containing EBVs, Deregression is undertaken and deregressed EVC, deregressed reliabilities and weights are outputted.imputation
Bash script that allows you to run BEAGLE v3, v4, and FIMPUTE using PLINK format binary input files.accuracy_imputation
comprehensive function for computing imputation accuracy. Accuracy has been computed as % correct, allelic error rate, correlation and correlation based on centered and scaled genotypes.Parentassigment_OHm
Parentage assignment using opposite homozygote methods.ROHs
Generate binary runs of homozygosity files from PLINK output and making ROH plots per sample and averageshaplos_analysis
Using haplotype blocks defined by Haploview and phased data, build the haplotype counts (change haplotypes into copies 0,1,2). Compute Genomic relationships based on the haplotypesLove Open Source and this site? Check out how you can help us