I am new to tumor phylogenetics. I want to call snvs from the tumor cells and using the snvs to build the phylogenetic trees. I found that currently there are two ways to call somatic mutations from tumor samples.
One is doing the somatic calling using somatic caller (MuTect2, Varscan ..).
Another way is doing the snvs calling using the germline calling software (GATK...)and then selected the positions which are 0/0 in normal tissue and 0/1 or 1/1 in tumor tissue.
Is there a huge difference between the results of these two methods? Which method is more accurate?
Appreciate for any help.