Dear GATK Team,
I have written a pipeline for variants identification in cancer exomes. It uses docker technology and both gatk3 and gatk4 that are automatically downloaded by docker hub to build the container. Unfortunately, now gatk3 is not more downloadable from your site.
Is there any way to download it automatically because it cannot be downloaded from google cloud platform? Or do gatk4 have an alternative to the CombineVariants command that I use in gatk3?
And for RealignerTargetCreator and IndelRealigner commands?
Thanks in advance
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