the algorithm of HC between gatk-3.7 and gatk-4.0 is almost same, you can see from: https://gatkforums.broadinstitute.org/gatk/discussion/10925/9-things-youve-been-dying-to-know-about-the-haplotypecaller-paper.
Q: How does the methodology compare to GATK4?
A: The GATK engine that parses the BAM and “shards” the data to pass to the tools has been rewritten for improved efficiency over GATK3, and the HaplotypeCaller code has been refactored for better organization and readability. So there's a lot that is different in terms of software implementation. However the algorithms and equations presented in the manuscript remain the same, so overall the paper's description of how the HaplotypeCaller operates also applies to the GATK4 beta version, and it is appropriate to use it as a citation for results derived from versions up to the current beta (4.beta.6).