I have a single multisample (48 samples) sample VCF file generated by GATK joint genotyping. I have further filtered by site level quality and such. Of these 48 samples, 24 samples are control and 24 samples are treatment. I am not so much interested between my samples vs reference. I am interested in variants that differ between my control and treated samples. How do I go about doing this? What is the workflow? What tools should I use?