soloboan/Multi-trait_simulations

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Created almost 8 years ago
Updated about 7 years ago

soloboan/Multi-trait_simulations

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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 implemented

dEBV_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 averages

selindexaccuracy

based on selection index formulaes, computed expected accuracies of selection when information source comes from mass, progeny, full-sib, hal-sibs, parents, etc

haplos_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 haplotypes