I will soon receive WGS data for 2 Rhesus Macaques, on which I want to call variants.
I intended follow GATK Best Practices. Creating the BAM files is fine but I'm unsure how to proceed to call somatic mutations using GATK4 Mutect2. Mutect2 requires either a tumor/sample paired set (I have 1 sample per macaque) or can be run in tumor only mode if one has (or can create) a panel of norms (PON). PONs are created with at least 40 samples - I have 2. Also, there is no known rhesus macaque variant .vcf in the public domain. I'm not sure if I should just use HaplotypeCaller or stick to Mutect2 and create a PON on the 2 samples i have.
Any advice/directions would be very welcome
EDIT: further details on experimental design added below
EDIT 2: Everyone was helpful in turning on the light here. My mistake was not understanding the difference between somatic and germline variant calling.