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GATK 2.8 was released on December 6, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Note that this release is relatively smaller than previous ones. We are working hard on some new tools and frameworks that we are hoping to make available to everyone for our next release.
Improved the indexing scheme for gVCF outputs using the reference calculation model.
The reference calculation model now works with reduced reads.
Disable tranche plots in INDEL mode.
Various VQSR optimizations in both runtime and accuracy. Some particular details include: for very large whole genome datasets with over 2M variants overlapping the training data randomly downsample the training set that gets used to build; annotations are ordered by the difference in means between known and novel instead of by their standard deviation; removed the training set quality score threshold; now uses 2 gaussians by default for the negative model; numBad argument has been removed and the cutoffs are now chosen by the model itself by looking at the LOD scores.
Added calculation for GC content.
Added an option to filter the bases based on their quality scores.
SplitSamFile now produces an index with the BAM.
Length metric updates to QualifyMissingIntervals.
Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT