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GATK 2.3 was released on December 17, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Soft clipped bases are no longer counted in the delocalized BQSR.
The user can now set the maximum allowable cycle with the --maximum_cycle_value argument.
Minor (5%) run time improvements to the Unified Genotyper.
Fixed bug for the indel model that occurred when long reads (e.g. Sanger) in a pileup led to a read starting after the haplotype.
Fixed the performance of GENOTYPE_GIVEN_ALLELES mode, which often produced incorrect output when passed complex events.
Fixed the interaction with the allele biased downsampling (for contamination removal) so that the removed reads are not used for downstream annotations.
The FisherStrand annotation ignores reduced reads (because they are always on the forward strand).
Can now be run multi-threaded with -nt argument.
Fixed bug where sometime the start position of a reduced read was less than 1.
ReduceReads now co-reduces bams if they're passed in toghether with multiple -I.
A brand new version of the per site down-sampling functionality has been implemented that works much, much better than the previous version.
More efficient initial file seeking at the beginning of the GATK traversal.
Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT