I have WGS dataset which are based on TGCA tumor normal samples. I have to call somatic mutations with various callers. So far, I have called mutations with Somatic Sniper, Mutest and VarScan. For VarDict, It has been required a BED file for specifying regions.
I want to be consistent with my method, I have to check mutations in whole sample instead of a given region. Therefore is there a way to call mutations without giving specific regions as an input?
Thank you for your help.