Why the Allele frequency changed when using different variant calling tools?

Question

[murali]

I am doing variant calling for a sample using SAMtools, GATK, Platypus, Freebayes. I observed the allele frequency generated by different tools varies for the some of variants. The allele frequency has to be same , but why it is changing?

Answer 1

[Pierre Lindenbaum]

"allele frequency has to be same" : that is not true if the  min/max criteria for "base quality"/"read quality"/"read flags", etc...  are not the same