I have 4 cancer cell lines exomes that I am trying to run with GATK. They are all breast cancer cell line subtypes. I have called the variants on them individually. I was wondering if it is more advisable to call the variants together or it is better to call variants individually. Along the same lines should I do joint genotyping on them.
Here is a doc that has information on steps to call somatic variants. Mutect2 is the tool used to call these variants and more info on that can be found here.