Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Release notes for GATK version 2.8

ebanksebanks Posts: 671GSA Member mod
edited March 17 in Announcements

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.
Post edited by Geraldine_VdAuwera on

Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

Comments

  • LouisBLouisB Broad InstitutePosts: 25Member, Third-party Developer, GSA Collaborator, Broadie

    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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,293Administrator, GSA Member admin

    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.

    Geraldine Van der Auwera, PhD

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