Version History
The current version is 3.6


These articles highlight the key improvements in major and minor version releases (for example, 3.4) and explain their significance. To view a complete list of changes per release (including minor changes and bug fixes), please see the release notes (next tab).
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 Note: There are no version highlights available for versions earlier than 2.2.

These are the release notes issued for all major and minor version releases (for example, 3.4). At this time, we do not provide release notes for subversion changes (for example, 3.4-46) but they are typically accompanied by a blog post, and you can view the latest changes in the Change log (next tab).
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 Note: There are no release notes available for versions earlier than 2.0.

These are the latest commit messages logged in the Github repository. Commit messages are short summaries that describe the changes made to the codebase. You can view the complete development history here.

Commit dateSummary
31st May 2016 Update pom versions for the 3.6 release
31st May 2016 Merge remote-tracking branch 'unstable/master'
31st May 2016 Merge pull request #1394 from broadinstitute/gvda_add_colt_dependency
31st May 2016 Add colt > cern.jet.normal dependency
31st May 2016 Merge pull request #1391 from broadinstitute/rhl_htsjdk_picard_2.4.1
3rd May 2016 Move Move htsjdk and picard to version 2.4.1
3rd May 2016 Merge pull request #1392 from broadinstitute/gvda_vqsr_retries_mdp
3rd May 2016 Ability to retry building VQSR model (contributed by mdp)
3rd May 2016 Merge pull request #1387 from broadinstitute/gvda_gatkdocs_enhancements
2nd May 2016 GATKDocs overhaul
2nd May 2016 Merge pull request #1388 from broadinstitute/gvda_disable_phone_home
2nd May 2016 Remove Phone Home
2nd May 2016 Merge pull request #1374 from broadinstitute/gvda_move_ReassignOrigin…
2nd May 2016 Add M2 to the HC annotations check
2nd May 2016 Improved article linking in error messages
2nd May 2016 Hide deletion arguments in ASEReadCounter
2nd May 2016 Fixed warnings in LAATV and ValidateVariants
2nd May 2016 Move indel realignment to public
2nd May 2016 Moved post-IR MQ reverter filter to public
2nd May 2016 Merge pull request #1377 from broadinstitute/vrr_non_ref_likelihood_r…

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Click here to view older changes on Github

For 2.x releases, we collected the Guide documentation into a Guide Book in PDF format. Each Guide Book release was versioned, so if you performed some analyses with an older version of the GATK, you can go back and look at the documentation that matched that version exactly. Note however that the Tool Documentation (GATKDocs, containing detailed argument lists) was not included in the versioned Guide Book since it can be generated directly from the source code. We currently have no immediate plans to generate PDF Guide Books for 3.x versions due to low apparent interest from the community, but let us know if you think we should resurrect this feature.


 Note: There are no PDF files of the Guide Book available for versions earlier than 2.3-9.