Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Release notes for GATK version 2.5

ebanksebanks Posts: 671GSA Member mod
edited May 2013 in Announcements

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

Reduce Reads

  • 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 support to reduce reads to CallableLoci.
  • 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.
Post edited by Geraldine_VdAuwera on

Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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