What are the plans for the tools available in Picard 2.9.2 or GATK3.7 that are not in GATK4 alpha? Is the plan eventually to port everything to GATK4? Or are some being permanently sent out to pasture?
I have specifically noticed as missing:
- CollectVariantCallingMetrics
- SetNmMdAndUqTags
- the -gvcf option for ValidateVariants