HAPPI.GWAS results not the same as GAPIT3

[jrod55]

Hi,

I've run FarmCPU using the demo data provided using the command below, and run the same analysis using GAPIT within R, matching the same options as the Demo_FarmCPU.yaml file. Though the results are similar, there are in fact some differences.

Using HAPPI GWAS:
Rscript HAPPI_GWAS.R -GAPIT Demo_FarmCPU.yaml

Within R:
library(GAPIT3)
phenos = read.table("mdp_traits.txt", header = TRUE)
myGAPIT <- GAPIT(
Y=phenos,
Model.selection = TRUE,
model=c("FarmCPU"),
SNP.MAF = 0.05,
ncpus = 20,
file.G="mdp_genotype_chr",
file.Ext.G="hmp.txt",
file.from=1,
file.to=10,
file.path="./Demo/"
)

Is there a reason for differences in results if presumably the same model should be being fit?

Thank you,
Jonas