The latest GATK release came out a few weeks ago, with changes corresponding to the period of April 13, 2022 - October 13, 2022. This update brings a ton of new tools to GATK, and we highly recommend updating to the newest version in order to take full advantage of them.

As always, the full GATK release notes are available on the GATK GitHub, but here is a small subsection of what's new in GATK 4.3.0.0:

• Support for Ultima Genomics: Added support for the Ultima Genomics flow-based sequencing platform. This adds a new --flow-mode argument to HaplotypeCaller and Mutect2 which better supports flow-based calling. In addition, a medley of new tools were added, including:

  • FlowFeatureMapper for quick heuristic calling of BAMs for diagnostics.

  • GroundTruthReadsBuilder to generate ground truth files for Basecalling.

  • HaplotypeBasedVariantRecaller for recalling VCF files using the HaplotypeCallerEngine.

  • SplitCram for breaking up CRAM files by their blocks.

   

• New tools for variant calling: Added a new suite of next-generation of tools for variant filtration based on site-level annotations, including:
  • ExtractVariantAnnotations: extracts site-level variant annotations, labels, and other metadata from a VCF file to HDF5.
  • TrainVariantAnnotationsModel: trains a model for scoring variant calls based on site-level annotations.
  • ScoreVariantAnnotations: scores variant calls in a VCF file based on site-level annotations using a previously trained model.
• New tools for reference comparison: As the name implies, we've added some powerful new ways to compare references:
  
  • CompareReferences is a new tool for analyzing the differences between references at both the dictionary and the base level. Functionality can be edited depending on the options selected, but in its default mode, CompareReferences can use reference dictionaries to generate an MD5-keyed table comparing the specified references, and does an analysis to summarize the differences between the references provided.
  • CheckReferenceCompatibility is a new tool to check BAM/CRAM/VCF files for compatibility against a set of references. This tool generates a table analyzing the compatibility of these input files against the provided references.
• New tools for SV Calling: Several new tools for SV Calling:
  • CondenseDepthEvidence is a new tool that combines adjacent intervals in DepthEvidence files.
  • LocusDepthtoBAF is a new tool that merges locus-sorted LocusDepth evidence files, calculates the bi-allelic frequency (BAF) for each sample and site, and writes these values as a BafEvidence output file.
  • PrintReadCounts is a new tool that prints (and optionally subsets) an read depth (DepthEvidence) file or a counts file as one (or more, for multi-sample DepthEvidence files) counts files for CNV determination.
• Mutect and HaplotypeCaller: Additional options and enhancements to HaplotypeCaller and Mutect2:
  • Added an optional "Pileup Detection" step to Mutect2 and HaplotypeCaller before assembly, that supplements the variants from local assembly with variants that show up in the pileups.
  • A few Mutect3 dataset enhancements were added, including an optional truth VCF for labels, and seq error likelihood annotation.
  • Added Mutect3 dataset generation to the Mutect2 WDL.
  • HaplotypeCaller now has two new likelihood models.