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GATK 2.6 was released on June 20, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Important note: with this release the GATK has officially moved to using Java 7.
Small runtime performance improvements contributed by Michael McCowan.
Added fix for the "Removed too many insertions, header is now negative" bug.
Runtime performance improvements when calling indels; calling indels in a single sample is almost 2x faster in our tests.
Fixed bug for bad AD values in some cases.
We have been working hard to reduce the number of false negatives (i.e. missed sites) for the Haplotype Caller and as such added a bunch of improvements to this tool. The sensitivity is now better than that of the Unified Genotyper is all of our whole genome tests for both SNPs and indels. Feel free to peruse the detailed version history for more information.
The Haplotype Caller now annotates IDs from dbSNP properly.
Added an overall genotype concordance metric to the output.
Fixed a bug in the printout of molten data in how it treated the genotypes.
Diagnose Targets now has an option to output missing intervals.
Fixed bug where sometimes intervals were emitted out of order.
Fixed bug for reads with indel CIGAR operators (I or D) at the start/end of the read.
Introduced a new tool, AnalyzeCovariates, to generate the BQSR quality assessment plots as a separate step, instead of doing it through the BaseRecalibrator.
The RMSMappingQuality annotation now works properly with reduced reads.
The various rank sum tests no longer use reduced reads in their calculations (because those reads do not represent distinct observations).
James Warren contributed a patch to have references with non-suffix ".fa" parse correctly.
We now emit the GATK version number in the header of VCFs that we produce.
Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT