I have exome sequencing data from tumor samples from mice with only one of them has tumor/normal tissue sequence. All the mice share the same genetic background, bred together and i believe they come from the same mother (not 100% sure about the same mother though). I have aligned them sequences using BWA-mem, marked the duplicates, etc.., and now want to call the variants either using VarScan somatic or GATK MuTect2. Is it possible to use this normal tissue sequence as a common Normal tissue for the other tumor sequences from the other mice? or is it better to call the tumors and the normal sequences individually then filter the Germline Variants afterwards from the Tumor samples?
Thanks in advance