GATK 2.8 was released on December 6, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history

Note that this release is relatively smaller than previous ones. We are working hard on some new tools and frameworks that we are hoping to make available to everyone for our next release.


Unified Genotyper

  • Fixed bug where indels in very long reads were sometimes being ignored and not used by the caller.

Haplotype Caller

  • Improved the indexing scheme for gVCF outputs using the reference calculation model.
  • The reference calculation model now works with reduced reads.
  • Fixed bug where an error was being generated at certain homozygous reference sites because the whole assembly graph was getting pruned away.
  • Fixed bug for homozygous reference records that aren't GVCF blocks and were being treated incorrectly.

Variant Recalibrator

  • Disable tranche plots in INDEL mode.
  • Various VQSR optimizations in both runtime and accuracy. Some particular details include: for very large whole genome datasets with over 2M variants overlapping the training data randomly downsample the training set that gets used to build; annotations are ordered by the difference in means between known and novel instead of by their standard deviation; removed the training set quality score threshold; now uses 2 gaussians by default for the negative model; numBad argument has been removed and the cutoffs are now chosen by the model itself by looking at the LOD scores.

Reduce Reads

  • Fixed bug where mapping quality was being treated as a byte instead of an int, which caused high MQs to be treated as negative.

Diagnose Targets

  • Added calculation for GC content.
  • Added an option to filter the bases based on their quality scores.

Combine Variants

  • Fixed bug where annotation values were parsed as Doubles when they should be parsed as Integers due to implicit conversion; submitted by Michael McCowan.

Select Variants

  • Changed the behavior for PL/AD fields when it encounters a record that has lost one or more alternate alleles: instead of stripping them out these fields now get fixed.

Miscellaneous

  • SplitSamFile now produces an index with the BAM.
  • Length metric updates to QualifyMissingIntervals.
  • Provide close methods to clean up resources used while creating AlignmentContexts from BAM file regions; submitted by Brad Chapman.
  • Picard jar updated to version 1.104.1628.
  • Tribble jar updated to version 1.104.1628.
  • Variant jar updated to version 1.104.1628.

Return to top

LouisB


Two things. 1. This post needs a release notes tag, it doesn't show up in the list of release notes. 2. I think there might be a few changes missing from the release notes. I don't believe the Queue update from scala 2.9 -> 2.10 was included in any of 2.7 releases, but it is in the 2.8. It should be mentioned somewhere since is has the potential to break existing scripts.

Fri 6 Dec 2013

Geraldine_VdAuwera


Thanks for pointing this out, Louis. I've added the tag so it should show up now (when the website cache resets). Regarding your second point, historically we haven't included changes to Queue in the GATK release notes, but we agreed today in group meeting that it would be a good idea to start doing so going forward.

Fri 6 Dec 2013



Fri 6 Dec 2013


At a glance



Follow us on Twitter

GATK Dev Team

@gatk_dev

@atogey Yes, that's what we've been doing. Still do most development locally but production/routine work go to cloud.
20 Mar 17
I added a video to a @YouTube playlist https://t.co/aEyEN4wnBj MPG Primer: Sequencing and Variant Discovery Pipelines (2016)
20 Mar 17
I added a video to a @YouTube playlist https://t.co/nEfmZ9u8sH Broad Institute — GATK in the Cloud: Running genomics pipelines at
20 Mar 17
RT @phosphorus: In case you missed our Meetup!Broad Institute: GATK in the Cloud: Running genomics pipelines at any scale: https://t.co/LQa
20 Mar 17
Updated #GATK Presentations page now links directly to archive of slide decks + YouTube playlists #foreveruptodate https://t.co/QCbos5KBWw
20 Mar 17

Our favorite tweets from others

From the @gatk_dev page describing .vcf files: "Don't write home-brewed VCF parsing scripts. It never ends well” https://t.co/28KcRoV14j
28 Feb 17
Our 3-day course on GATK https://t.co/mtN60KRTyS finished - 38 participants very happy! Big thanks to @gatk_dev team for excellent lessons.
24 Feb 17
@froggleston @dgmacarthur Sounds like ExAC is reaching Uber stage. ‘Uber but for pizza’. ‘ExAC but for wheat’.
14 Jan 17
#ESRenpeinture grad school - postdoc - after postdoc https://t.co/o3vQMgBDgk
6 Jan 17
Really happy to have you again this year! @VIBLifeSciences https://t.co/8rg5VQ2fbX
3 Jan 17
See more of our favorite tweets...
Search blog by tag

appistry ashg ashg16 benchmarks best-practices bug bug-fixed cancer cloud cluster cnv collaboration commandline community compute conferences cram cromwell depthofcoverage diagnosetargets error forum gatk3 gatk4 genotype-refinement genotypegvcfs google grch38 gvcf haploid haplotypecaller hg38 holiday hts htsjdk ibm intel java8 job job-offer jobs license meetings mutect mutect2 ngs outreach pairhmm parallelism patch performance picard pipeline plans ploidy polyploid poster presentations printreads profile promote release release-notes rnaseq runtime saas script sequencing service slides snow speed status support syntax talks team terminology topstory troll tutorial unifiedgenotyper vcf-gz version-highlights versions vqsr wdl webinar workflow workshop xhmm