GATK 3.3 was released on October 23, 2014. Itemized changes are listed below. For more details, see the user-friendly version highlights.

Haplotype Caller

• Improved the accuracy of dangling head merging in the HC assembler (now enabled by default).
• Physical phasing information is output by default in new sample-level PID and PGT tags.
• Added the --sample_name argument. This is a shortcut for people who have multi-sample BAMs but would like to use -ERC GVCF mode with a particular one of those samples.
• Support added for generalized ploidy. The global ploidy is specified with the -ploidy argument.
• Fixed IndexOutOfBounds error associated with tail merging.

Variant Recalibrator

• New --ignore_all_filters option. If specified, the variant recalibrator will ignore all input filters and treat sites as unfiltered.

GenotypeGVCFs

• Support added for generalized ploidy. The global ploidy is specified with the -ploidy argument.
• Bug fix for the case when we assumed ADs were in the same order if the number of alleles matched.
• Changed the default GVCF GQ Bands from 5,20,60 to be 1..60 by 1s, 60...90 by 10s and 99 in order to give finer resolution.
• Bug fix in the exact model when calling multi-allelic variants. QUAL field is now more accurate.

RNAseq analysis

• Bug fixes for working with unmapped reads.

CalculateGenotypePosteriors

• New annotation for low- and high-confidence possible de novos (only annotates biallelics).
• FamilyLikelihoodsUtils now add joint likelihood and joint posterior annotations.
• Restricted population priors based on discovered allele count to be valid for 10 or more samples.

DepthOfCoverage

• Fixed rare bug triggered by hash collision between sample names.

SelectVariants

• Updated the --keepOriginalAC functionality in SelectVariants to work for sites that lose alleles in the selection.

PrintReads

• Read groups that are excluded by sample_name, platform, or read_group arguments no longer appear in the header.
• The performance penalty associated with filtering by read group has been essentially eliminated.

Annotations

• StrandOddsRatio is now a standard annotation that is output by default.
• We used to output zero for FS if there was no data available at a site, now we omit FS.
• Extensive rewrite of the annotation documentation.

Queue

• Fixed Queue bug with bad localhost addresses.
• Fixed issue related to spaces in job names that were fine in GridEngine 6 but break in (Son of) GE8.
• Improved scatter contigs algorithm to be fairer when splitting many contigs into few parts (contributed by @smowton)

Documentation

• We now generate PHP files instead of HTML.
• We now output a JSON version of the tool documentation that can be used to generate wrappers for GATK commands.

Miscellaneous

• Output arguments --no_cmdline_in_header, --sites_only, and --bcf for VCF files, and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files moved to the engine level.
• htsjdk updated to version 1.120.1620