GATK 3.1 was released on March 18, 2014. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history


Haplotype Caller

  • Added new capabilities to the Haplotype Caller to use hardware-based optimizations. Can be enabled with --pair_hmm_implementation VECTOR_LOGLESS_CACHING. Please see the 3.1 Version Highlights for more details about expected speed ups and some background on the collaboration that made these possible.
  • Fixed bugs in computing the weights of edges in the assembly graph. This was causing bad genotypes to be output when running the Haplotype Caller over multiple samples simultaneously (as opposed to creating gVCFs in the new recommended pipeline, which was working as expected).

Variant Recalibrator

  • Fixed issue where output could be non-deterministic with very large data sets.

CalculateGenotypePosteriors

  • Fixed several bugs where bad input were causing the tool to crash instead of gracefully exiting with an error message.

Miscellaneous

  • RandomlySplitVariants can now output splits comprised of more than 2 output files.
  • FastaAlternateReferenceMaker can now output heterozygous sites using IUPAC ambiguity encoding.
  • Picard, Tribble, and Variant jars updated to version 1.109.1722.

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Mon 17 Mar 2014


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New #GATK web address: https://t.co/SmXppw36ir (but www links or bookmarks will still work) https://t.co/PqbYbGhSWH
20 Jul 16
@yokofakun GenomeSTRiP is developed by a different group (Bob Handsaker at Harvard); expect Bob to answer on the forum.
18 Jul 16
@TechnicalVault and we're currently working on a public roadmap document for GATK4 (2/2)
11 Jul 16
@TechnicalVault Happy to discuss roadmap, not meant to be secret. We try to post updates on blog, eg https://t.co/1xKZXf3dLu (1/2)
11 Jul 16
@biobenkj @torstenseemann @broadinstitute Post question to #GATK forum -> will be answered. https://t.co/bEGBZUtyjL
11 Jul 16

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You’re right @gatk_dev honesty is key! About variants manual filtering: “In any case you're probably in for a world of pain.” Ha now I know!
11 Jul 16
.@gatk_dev I like the new documentation index page, the subheading has made my day! :D #doge #GeekHumourFTW https://t.co/9RXnDTMoBm
8 Jul 16
There is no NGS, NG is today so should only be called high-throughput sequencing #CSC #GATKworkshop https://t.co/paHcNimD7o
16 Jun 16
The @dgmacarthur lab leaving as they came, rock stars of science in their stretch limo https://t.co/IQ0eCOT5H6
14 May 16
Hey @BroadGenomics we just flew past 250,000 exomes + genomes. Good job everyone.
13 May 16
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