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Multi-threaded support in the BaseRecalibrator tool has been temporarily suspended for performance reasons; we hope to have this fixed for the next release.
Implemented support for SOLiD no call strategies other than throwing an exception.
Renamed the per-sample ML allelic fractions and counts so that they don't have the same name as the per-site INFO fields, and clarified the description in the VCF header.
UG now makes use of base insertion and base deletion quality scores if they exist in the reads (output from BaseRecalibrator).
Added LowQual filter to the output when appropriate.
Added some support for calling on Reduced Reads. Note that this is still experimental and may not always work well.
Fixed bug where reads were soft-clipped beyond the limits of the contig and the tool was failing with a NoSuchElement exception.
Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out.
Fixed support in the AlleleCount stratification when using the MLEAC (it is now capped by the AN).
Fixed incorrect allele counting in IndelSummary evaluation.
Now outputs the first non-MISSING QUAL, instead of the maximum.
Now supports multi-threaded running (with the -nt argument).
Fixed behavior of the --regenotype argument to do proper selecting (without losing any of the alternate alleles).
No longer adds the DP INFO annotation if DP wasn't used in the input VCF.
Updated and improved the BadCigar read filter.
GATK now generates a proper error when a gzipped FASTA is passed in.
Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT