I noticed there was VariantAnnotator in the previous version of GATK from the website but not available in GATK 3.3. How to perform this task in GATK3.3?
VariantAnnotator is still available in GATK 3.3. It's not designed for designing PCR primers, however.
Unfortunately, ValidationAmplicons has been removed from GATK.
Thanks for you reply. Sorry, I made a mistake. There was ValidationAmplicons in the previous version of GATK. Is ValidationAmplicons still available in GATK 3.3?