There are many softwares that can call tumor normal pairs easily. However, in a real clinical setting, we only have tumor sample, and likely on FFPE slides.
Does anyone have any suggestions one single tumor sample variant calling pipelines without normals? I know some softwares like MuTect do have single sample mode, but likely to have many junks b/c it's not designed to do so. I am looking for more complicated tools, like the one FoundationOne is using.