The latest GATK release is out, with changes corresponding to the period of October 10, 2020 - February 18, 2021. The full GATK release notes are available on the GATK GitHub, but here is just a taste of what's new in GATK 4.2.0.0:

• DRAGEN-GATK: We've been working closely with Illumina in order to port a number of tools from their DRAGEN pipeline into GATK, specifically for germline short variant calling. These tools will form the basis of the upcoming open-source DRAGEN pipeline implementation which we are calling DRAGEN-GATK. This is part of a much bigger release, so see this blog post for more information about these exciting developments.

  • We recommend that most users wait until the full DRAGEN-GATK pipeline is released as a WDL workflow before evaluating these new features. However, high-level users are currently able to implement DRAGEN-ported tools into their own pipelines, including DragSTR (for adjusting HMM indel priors with better indel calling) and two new genotyper error models (Base Quality Dropout BQR and Foreign Read Detection FRD).
• HaplotypeCaller: We've added bugfixes and improvements to HaplotypeCaller to improve the phasing of variant calls, and to fix edge cases with indels and spanning deletions.
• CNV Calling: A new pipeline for gCNV exome joint calling, including the JointGermlineCNVSegmentation tool (and associated workflow joint_call_exome_cnvs.wdl) to combine gCNV segments and calls across samples.

 In addition, we've fixed bugs and added features in a number of areas, including:

• SV Calling: New PrintSVEvidence tool for printing Structural Variation evidence file types (RD, PE, SR, BAF), which is frequently used in the GATK-SV pipeline.

• GenomicsDB: New feature for GenomicsDBImport for boosting performance when using massive numbers of contigs.

• Mutect2: Bugfixes and improvements to Mutect2, Funcotator and mitochondrial pipelines.

These changes, and more, are explained in the full GATK release notes.