BLUPF90 Scripts for Genetic Analysis of Goose Steatosis Traits

This repository contains example scripts for estimating genetic parameters using the BLUPF90 software suite. The scripts handle up to four traits simultaneously (from the 15 available in the dataset data.txt found at https://doi.org/10.57745/4MI9JN ). script1.sh runs renumf90 using the parameter file renum_ex1.par. This file processes the traits LW, AFW, CW, and BMW. The model includes the effects of animal, sex, and slaughter date. Optional instructions allow blupf90+ to compute variance ratios and their standard errors. script2.sh follows a similar structure but analyzes the traits LW, BW14r, and BW26. In this case, the fixed effects used in the model are different. script3.sh runs a bivariate analysis, using a categorical data (LCAT) to describe the liver. Hence, it calls gibbsf90+ instead of blupf90+. Pay attention to the missing value code, which must be 0. gibbs_samples.R is a R program to read the output from gibbsf90+. One must provide the number of estimated components (here NCOMP = 6) and the program computes the variance ratios and their posterior distributions.