The latest GATK release is out, with changes corresponding to the period of July 30, 2021 - August 18, 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 4.2.2.0:

We're pushing out a smaller update this time, which includes changes that are mainly focused around improving our Processing Pipeline.

• New Tools: ShiftFasta is a new tool that creates a FASTA file with the bases shifted by an offset

• ReblockGVCF: ReblockGVCF is now out of beta, with several important improvements! This tool can be used to postprocess HaplotypeCaller GVCFs to decrease filesize, and outputs now eliminate overlapping reference blocks/gaps following trimmed deletions. Additionally, fixes have been made that are associated with input no-call genotypes, an off-by-one error at contig starts, an error on ref blocks with missing DPs (if --floor-blocks arg is not provided), and a bug in rare cases where spanning deletion (*) allele was incorrectly modified.

• Mutect2: FilterMutectCalls has a new --microbial-mode argument. By activating Microbial Mode, you can set filters to defaults that are appropriate for microbial calling.
• ValidateVariants: Added an optional argument to check for GVCF reference blocks overlapping variants or other reference blocks.
• Bug Fixes: Fixed bugs in Funcotator(which prevented Match_Norm_Seq_Allele1 and Match_Norm_Seq_Allele2 fields populating in MAF output), as well as a bug in DRAGEN-GATK's  CalibrateDragstrModel that could cause intermittent ArrayIndexOutOfBoundsExceptions.

Additional changes were made to the Mitochondrial Pipeline, CNV Calling, and more — they are explained in the full GATK release notes.