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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@iskander @NJL_NGS Treat them like any other read, no special handling. Problems arise in CIGAR functions that don’t know how to handle Ns.
7 Dec 16
@iskander @NJL_NGS By default we error out. Possible to override using -U ALLOW_N_CIGAR_READS but tool may crash. Is unsupported usage.
7 Dec 16
RT @geoffjentry: How @WDL_dev empowers a biochemist w/o programming background to perform large scale genomics analyses: https://t.co/BxAnK
6 Dec 16
@iskander @NJL_NGS Not aware of any, sorry.
5 Dec 16
@NJL_NGS @iskander No, GATK tools don't handle Ns in CIGAR, splitting is obligatory. See RNAseq guidelines in docs for more details.
5 Dec 16

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