## Release notes for GATK version 2.5

### Posted by ebanks on 30 Apr 2013 (4)

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

• DRASTIC improvements in the compression algorithm plus myriad bug fixes. Too many to list here; see detailed version history for more information.

## Unified Genotyper

• Fixed bug for indel calling with really long reads (assigning the wrong genotypes).
• Automatic contamination fixing now works on reduced reads.
• Fixed rare bug in the general ploidy SNP likelihood model when there are no informative reads in a pileup.
• Fixed bug where haplotypes with 0 bases were being created.
• Fixed problem where our internal PairHMM was generating positive likelihoods.

## Haplotype Caller

• 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).
• Fixed problem where our internal PairHMM was generating positive likelihoods.
• Can now write BAMs showing the assembled haplotypes.

## Diagnose Targets

• 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 bug where intervals were skipped when they were not covered by any reads.

## Base Recalibrator

• 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 for RNA seq alignments with Ns.

## Select Variants

• 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.
• Fixed bug where maxIndelSize argument wasn't getting applied to deletions.

## Variant Annotator

• Added support for snpEff "GATK compatibility mode".
• Can now list available annotations by doing java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations
• QualByDepth remaps QD values > 40 to a gaussian around 30.
• Removed several deprecated annotations (AverageAltAlleleLength, MappingQualityZeroFraction, and TechnologyComposition) and others are no longer marked as experimental.

## Variant Filtration

• 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.

## Left Align Variants

• Renamed to LeftAlignAndTrimVariants.
• Added ability to trim common bases in front of indels before left-aligning.
• Added ability to split multiallelic records and then left align them.

## Miscellaneous

• 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.
• Fixed @PG tag uniqueness issue with BAMs we were producing.
• Fixed rare bug in GenotypeConcordance for multi-allelic sites.
• Added check for reads without stored bases (i.e. that use '*') which we do not support.
• Added a new walker to split MNPs into their allelic primitives (SNPs).
• We no longer allow the use of compressed (.gz) references in the GATK.
• Picard/Tribble/Variant jars updated to version 1.90.1442.

#### Geraldine_VdAuwera

FYI -- at time of posting, the release is in the pipe, so the packages should be available for download by the end of the day if all goes well. Version highlights will be available within a couple of days.

#### sbaheti

Is there a difference between version GATK 2.5 GATK 2.5-2, if there is any difference then where can i find the version differences b/w the two. Thanks Saurabh

#### Geraldine_VdAuwera

No, 2.5-2 was the first publicly released version of GATK 2.5. Sometimes there are jumps between -dash version numbers that are available to the public due to technical reasons.

#### droazen

The only difference between GATK 2.5 and 2.5-2 is some post-release cleanup we did related to our test infrastructure. You can see the exact changes in the commit logs to our github repository: [https://github.com/broadgsa/gatk-protected/commits/master](https://github.com/broadgsa/gatk-protected/commits/master) The topmost commit is 2.5-2 (the current release), the one below that is 2.5-1, and version 2.5 is the third commit from the top.

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