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 want to do whole exome sequencing of "tumor biopsies" from 12 mice (6 Ko and 6 ctrl). The main goal is to find difference in number and nature/patterns of mutations between the tumor samples from the ctl vs ko mice ( as non synonymous, synonymous, non coding, frequency of transitions, etc..)
as we believe the ko to be more protected (therefore should accumulate less number of mutation).
I would like to know your suggested depth of coverage (i initially thought about 100x at least), and a suggested analysis workflow would be much appreciated.
Thanks in advance.