i am a little bit new to whole exome seq analysis and did it only once before for human samples using bwa and Gatk pipeline and now I have whole exome sequencing data from tumor samples for C57BL/6 mice ( Gut tumor samples 3 wild type vs 3 KO). Unfortunately the mice aren't avialabe anymore and they didn't sequence parallel normal tissue. In Humans i would have compared it to 1000 genomes or something but what be the best way here to detect somatic SNVs in inbred mice. as most of the Pipeline i found like GATK MuTect2 run normal tissue parallel to the tumor samples?
My PI would like at the end to reach similar to the approach mentioned in this paper:- https://www.sciencedirect.com/science/article/pii/S153561081730507X?via%3Dihub).
Thanks in advance.