CatVariants, MergeVcfs or GatherVcfs
I have 35 WholeExome Samples (and it will be more soon). I called each of those chromosomewise which resulted in 35 * 25 = 875 g.vcfs. In a second step I used CombineGVCFs to merge the samples stepwise for each chromosome (=> 25 g.vcfs). My first idea for a next step was to use CombineGVCFs again to create one final g.vcf and do the genotyping. Since this takes longer than expected I looked around and found CatVariants which should be much faster (https://gatkforums.broadinstitute.org/gatk/discussion/3455/catvariants-or-combinevariants). With this tool I could genotype each chromosome and merge the vcfs in less time. But CatVariants doesn't seem to exist in GATK4 anymore. GATK4 has MergeVcfs and GatherVcfs.
Which tool is the best choice to merge vcfs that contain different chromosomes?
Is it a good idea to do the genotyping parallel and merge the vcfs instead of merging the g.vcfs and genotype the complete result file?
Are there other/better ways to do this? Should I use cobineGVCFs even though it is not that fast? And please don't say GenomicsDB. It is the slowest of them all on our local server.