The latest GATK release is out, with changes corresponding to the period of August 18, 2021 - November 2, 2021. As always, we highly recommend updating to the newest version, as it will help to correct bugs that may have an effect on your data.

The full GATK release notes are available on the GATK GitHub, but here is just a taste of what's new in GATK 4.2.3.0:

• Fixed a bug where Mutect2 failed to filter germline variants with alternate representations, causing variants with alternative representations in gnomAD to not be recognized as being the same as called variants in some cases.

• HaplotypeCaller and Mutect2 have a new --debug-assembly-variants-out diagnostic option. This outputs a side VCF with variants detected by assembly.

• GenomicsDB has been updated to GenomicsDB v1.4.2, which should fix some book-keeping errors, along with other improvements.
• In addition, GenomicsDB has two new arguments. The first argument, --call-genotypes,  enables the output of called genotypes when tools like CombineGVCFs and SelectVariants read from a GenomicsDB workspace. The second argument, --bypass-feature-reader, help to reduce memory usage and potentially speed up the import process — it will bypass the default Java implementation of the htslib VCF reader, in favor of a C-based implementation. 
• FilterFuncotations can now process multi-transcript genes.

• Support in CombineGVCFs and GenotypeGVCFs for "reblocked" GVCFs as produced by the ReblockGVCF tool. Reblocked GVCFs have a significantly reduced storage footprint.

• More control over the Smith-Waterman parameters in HaplotypeCaller, Mutect2, and FilterAlignmentArtifacts.

• A new Fragment Allele Depth (FAD) variant annotation similar to the AD annotation except that allele support is considered per read pair, not per individual read

• GenomicsDB bug fixes and enhancements

• Updated sqlite-jdbc library to a newer version to support Macs with M1 chips.
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