The latest GATK release is out, with changes corresponding to the period of June 20, 2020 - October 10, 2020. The full GATK release notes are available on the GATK GitHub, but here is just a taste of what's new in GATK 4.1.9.0:

• There are two new tools available: GeneExpressionEvaluation for evaluating gene expression from RNA-seq reads aligned to the genome, and ReferenceBlockConcordance for evaluating the concordance of reference blocks in GVCF files.

• This GATK update brings Funcotator up to the latest Gencode release, and fixes contig naming issues with dbSNP (leading to errors such as, for example, "hg38 dbSNP has incorrect contig names"). It also supports new tags, including the TAGENE gene tag and MANE_SELECT.

• Fixed an issue with FuncotateSegments where the default value of --alias-to-key-mapping was being set to an immutable value.

• Removed slow string formatting calls from DepthOfCoverage, leading to significant performance improvements. In a locally run test, using default arguments, the runtime for a full chr15 WGS dropped from 8.9 min to 4.7 min.

• Significantly improved performance of SelectVariants with large numbers of samples. In a test run with several thousand samples, the runtime dropped from 5 minutes to 6 seconds.
• This update includes important bug fixes to HaplotypeCaller and Mutect2 that caused loss of insertion events immediately following a deletion, as well as general bug fixes to CreateSomaticPanelOfNormals, and CombineGVCFs, among others.

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