Stick to 3.5 or change to 4.0?
Until now we were using version 3.5 of the GATK toolkit in our group. Since we start with a new project now we think about moving to 4.0. However, staying with 3.5 would be convenient due to comparability of results and processing times etc. and we could keep using all scripts without editing. Is it strongly recommended to switch or is 3.5 still fine? What are the "killer features" or highly important changes?
Thank you for answering,