Calling variants with frequency lower than 1%

[fa-vio]

Hello,

I tried to run Pisces and Scylla on a somatic sample with the option --minvf 0.005, in an attempt to call variants with frequency lower than 1%. But there were no results with VF lower than 0.01.

I used LoFreq on the same sample and it picked quite some results with frequency lower than 0.01. I am aware that most of them are likely to be false positives, but I was wandering if 0.01 is a strict lower bound for Pisces.

thanks in advance