reason Variations found in all the samples is the same

Question

[marzieh]

I did variant calling for several samples and used HaplotypeCaller but I do not know why the variations found in all the samples are exactly the same and there is no difference between them. Why did this happen? Please guide me

[Pierre Lindenbaum]

frequent variant or it's the same sample.

[cpad0112]

Probably code loop, parallelization or variables in the code didn't work, as expected.