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.
Fixed a bug where
Mutect2failed 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.
Mutect2have a new
--debug-assembly-variants-outdiagnostic 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
SelectVariantsread 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.
FilterFuncotationscan now process multi-transcript genes.
GenotypeGVCFsfor "reblocked" GVCFs as produced by the
ReblockGVCFtool. Reblocked GVCFs have a significantly reduced storage footprint.
More control over the Smith-Waterman parameters in
A new Fragment Allele Depth (
FAD) variant annotation similar to the
ADannotation except that allele support is considered per read pair, not per individual read
GenomicsDB bug fixes and enhancements
sqlite-jdbclibrary to a newer version to support Macs with M1 chips.
Additional changes were made to the GenotypeGVCFs / CombineGVCFs, CNV Calling, and more
— they are explained in the full GATK release notes.