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GATK 2.5 was released on April 30, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Fixed bug for indel calling with really long reads (assigning the wrong genotypes).
Automatic contamination fixing now works on reduced reads.
Comprehensive performance improvements to the accuracy of calling both SNPs and indels; runtime is also much improved (but still slower than the Unified Genotyper; we expect it to be faster than UG in the next release though). See detailed version history for more information.
Fixed bug for calling on reduced reads (counts were not being assigned correctly).
Significantly refactored this tool; it now works with a "plugin" system (see documentation for more information).
Fixed bug where LOW_MEDIAN_COVERAGE was output when no reads are covering the interval.
Fixed the tool to work correctly with empty BQSR tables.
Fixed issue where Print Reads was running out of disk space when using the -BQSR option even for small bam files.
Fixed bug where using the --exclude_sample_file argument was giving bad results.
Fixed bug when using the --keepOriginalAC argument which caused it to emit bad VCFs.
Added support for snpEff "GATK compatibility mode".
Can now list available annotations by doing
java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations
Don't allow users to specify keys and IDs that contain angle brackets or equals signs (which are not allowed in the VCF specification).
Added feature that allows one to filter sites outside of a given mask.
Renamed to LeftAlignAndTrimVariants.
Added ability to trim common bases in front of indels before left-aligning.
We removed the auto-creation of fai/dict files for fasta references because it was too buggy.
Fixed bug where we could fail to find the intersection of unsorted/missorted interval lists.
Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT