4.2.2.0
Download release: gatk-4.2.2.0.zip
Docker image: https://hub.docker.com/r/broadinstitute/gatk/
Highlights of the 4.2.2.0 release:
-
The
ReblockGVCF
tool is now out of beta with several important improvements. This tool can be used to postprocessHaplotypeCaller
GVCFs to decrease filesize. -
FilterMutectCalls
now has a--microbial-mode
argument that sets filters to defaults appropriate for microbial calling -
Important bug fixes to
CalibrateDragstrModel
andFuncotator
Full list of changes:
-
New Tools
ShiftFasta
: create a fasta with the bases shifted by an offset (#6694)
-
ReblockGVCF
ReblockGVCF
is now out of beta (#7419)- Improved
ReblockGVCF
output to eliminate overlapping reference blocks and reference gaps following trimmed deletions (#7122) - Fixed bugs associated with input no-call genotypes and fixed an off-by-one error at contig starts (#7404)
- Fixed an error on ref blocks with missing DPs (if
--floor-blocks
arg is not provided); fixed rare cases where spanning deletion (*) allele is incorrectly modified (#7400)
-
Mutect2
FilterMutectCalls
: added a--microbial-mode
argument that sets filters to defaults appropriate for microbial calling (#6694)
-
ValidateVariants
- Added an optional argument to check for GVCF reference blocks overlapping variants or other reference blocks (#7405)
-
DRAGEN-GATK
-
Funcotator
- Fixed an issue where the
Match_Norm_Seq_Allele1
andMatch_Norm_Seq_Allele2
fields were not being populated in MAF output (#7422)
- Fixed an issue where the
-
Mitochondrial pipeline
- Removed calls to
FilterNuMTs
andFilterLowHetSites
, which are no longer being used (#7325)
- Removed calls to
-
CNV Calling
- Fixed a bug resulting from prefix strings of less than 3 characters when creating temporary files in
GermlineCNVCaller
and improved documentation of corresponding utility methods. (#7411)
- Fixed a bug resulting from prefix strings of less than 3 characters when creating temporary files in
-
Documentation