Release notes for GATK version 2.8

Fri 6 Dec 2013
Share

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

Fri 6 Dec 2013
Share

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



Search blog by tag

2013 ad agbt14 appistry baserecalibrator belgium best-practices blog bqsr broken-links brussels bug bug-fixed cancer catvariants challenge combinegvcfs combinevariants commercial community compbio competition conferences depthofcoverage diagnosetargets documentation downtime error fastaalternatereferencemaker forum gatk gatk-3-0 gatk-3-1 gatk-3-2 gatk-lite gatk2 gatk3 genotypegvcfs gsa gsa-announce gvcf haplotypecaller hardware holiday indelrealigner intel job job-offer jobs joint-analysis joint-discovery key license lite media meetings multisample multithreading mutect nt optimization pairhmm paper performance phone-home pipeline poster presentations press printreads queue randomlysplitvariants readbackedphasing reducereads reference-model release release-notes rnaseq scatter-gather selectvariants slides spam splitncigarreads support talks topstory trivia tutorials unifiedgenotyper userstories validatevariants variantannotator varianteval variantrecalibrator variantstobinaryped version-highlights video videos webinar workshop


GATK Dev Team

@gatk_dev

RT @edgenome: Today's attendees at our 'Linux for Genomics' workshop. Keep tuned for more info on forthcoming courses and events... http://…
25 Jul 14
RT @TheAllium: Broad Institute “Can’t be bothered anymore” with donations below $200 Million http://t.co/KOLby8OlXA via @theallium
24 Jul 14
RT @appistry: Join us tomorrow for our #webinar discussing the #PickMyPipeline Challenge! #NGS http://t.co/iK4s52xpzf
23 Jul 14
New Pipeline Challenge from @Appistry http://t.co/m9jWWmRn9g
23 Jul 14
@Elfsevier @jermdemo Isn't bro-ness itself a disease? Or do you mean diseases that are comorbid to bro-ness?
22 Jul 14