I'm using GATK's GenotypeGVCFs tool to jointly genotype ~1000 samples. It's my understanding that because of the genome wide annotations that are calculated, I can't speed things up by using CombineVCFs on smaller jointly called groups. Am I correct?
Is there some way to speed up my joint genotyping with GATK?
edit: The reference genome we're using is only composed of scaffolds. We're worried that because our genome is only composed of scaffolds that this might be slowing things down. Is this thinking correct, or does GATK not care?