variant calling with biological replicates

I am new to use GATK pipeline for SNP calling. I am currently working on four different populations (RNASEq data) with 6 clones. Each clone has 3 biological replicates. How do I combine the variant calling step for the replicates?
I went through the GATK documentation on cohorts and stuff, but I am not sure if I should continue this.
Does combining the resultant vcf file also a possibility?
please help!