Release notes for GATK version 3.1

Mon 17 Mar 2014
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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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GATK Dev Team

@gatk_dev

@samstudio8 Fun and interesting blog post! Our docs team will clarify the filter doc; code holds ultimate answer https://t.co/pN50hHQ71Z
4 Sep 15
@gatoravi Thx :) Credit goes to wider DSDE team (of which we are a subset) https://t.co/fclufciDI4
4 Sep 15
@rtyags yes, totally fine with citation. If u can, let us know which fig(s) so we know what ppl find esp useful.
4 Sep 15
RT @erlichya: LOL! "Lior's blog is known for its specificity but less for its sensitivity" - @GenomeNathan intro to @lpachter seminar at @n…
27 Aug 15
RT @thatdnaguy: **VERY IMP. #GATK BUG WARNING** Do not run GenotypeGVCFs on gzipped and tabix indexed files. Increased runtime ** ~70X ** …
27 Aug 15