Output number of SNPs are chaging from run to run

Question

[Bioin]

Hi Biostars,

I am calling variations from GBS data using TASSEL-5.2. I ran the complete pipeline four times inputting the same data and key file for my surprise total number of variations from each run is slightly different. Is it quite normal or am I doing any mistake? any explanation would be greatly appreciated.

Thanks in advance.

[Mark]

please post your code or script you are running.