I have been trying to combine two VCF files with
file1.vcf with samples A,B,C and
file2.vcf with samples D,E,F. I tried tools like GatherVcfs, MergeVcfs, but they both fail. What is the right tool I should be using to do this? There was
CombineVariants tool in GATK3, which is not available in GATK4.