Hi, My input genotypic file (Hapmap format) contains 48425 SNPs, I have tried to filter in Tassel V.5 based on Minor Allele frequency filtering at 0.05 and got 42711 SNPs.

I have also checked from the site summary file of the tassel, there are 42707 SNPs with MAF > 0.05, 42711 SNPs with MAF >= 0.05, 41228 SNPs with MAF > 0.06.

Then I have used the same genotypic file (containing 48425 SNPs) in Gappit and it gave me 42952 SNPs after Minor Allele frequency filtering at 0.05.

Gappit code:

myGAPIT <- GAPIT(
  Y=myY,
  G=myG,
  PCA.total=6,
  SNP.MAF = 0.05,
  model=c("GLM","MLM","FarmCPU","Blink")
)

What could be the possible reason for this difference?