Is there a page, where I can see an example of what CombineVariants does with and without --printComplexMerges? I'm wondering whether to use bcftools merge or GATK CombineVariants.
Nope, sorry -- that's not documented at the moment. I'll add it to the to-do list but I wouldn't recommend holding your breath...
Thanks @Geraldine_VdAuwera. I'll run both with and without the argument on some real VCF files and post in this thread. It should happen within the next 3 weeks.
That would be lovely, thank you!