I have 4 RNA Seq samples from p53 wild type mouse(WT) and p53 knock out(KO) mouse (2 replicates each) which were treated with Tamoxifen .
these were analysed with sam tools to call variants. Variants were called for each of the WT and KO samples.(4 .vcf files)
my question is even though variants were found , is it genomically important to call variants on each of these 4 samples and are they biologically meaningful ?
Are variants only called on Tumour and Normal tissues or they can be called on an RNA seq transcription factor KO experiment?