196. Release notes for GATK version 31
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
created by ebanks
on 2014-03-17
GATK 3.1 was released on March 18, 2014. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Haplotype Caller
Haplotype Caller
- Added new capabilities to the Haplotype Caller to use hardware-based optimizations. Can be enabled with
--pair_hmm_implementation VECTOR_LOGLESS_CACHING. Please see the 3.1 Version Highlights for more details about expected speed ups and some background on the collaboration that made these possible. - Fixed bugs in computing the weights of edges in the assembly graph. This was causing bad genotypes to be output when running the Haplotype Caller over multiple samples simultaneously (as opposed to creating gVCFs in the new recommended pipeline, which was working as expected).
Variant Recalibrator
Variant Recalibrator
- Fixed issue where output could be non-deterministic with very large data sets.
CalculateGenotypePosteriors
CalculateGenotypePosteriors
- Fixed several bugs where bad input were causing the tool to crash instead of gracefully exiting with an error message.
Miscellaneous
Miscellaneous
- RandomlySplitVariants can now output splits comprised of more than 2 output files.
- FastaAlternateReferenceMaker can now output heterozygous sites using IUPAC ambiguity encoding.
- Picard, Tribble, and Variant jars updated to version 1.109.1722.
Updated on 2014-03-19