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Reasons to upgrade Picard

The version of Picard installed in my institution's cluster is version 1.112, which wasn't even listed on Github. Can anyone from the GATK team provide me reasons as for why should I ask the IT admin people to install the current version (2.5.0)? (JDK versioning doesn't count.)

Thanks in advance.


Issue · Github
by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Because new tools have been added, many existing tools have been enhanced and various bugs have been fixed. For a catalog of changes, see the version notes.
  • johnmajohnma Member

    Well, I wouldn't have to ask this question if I knew where the release notes were, but I didn't find any in github, at least not to me.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Sorry @johnma, when the weather gets stuffy, I get snappy. Anyway, each release posted here comes with a README file that details all the changes that have been made. Admittedly there are many releases and no effort has been made to make the notes end-user-friendly, so I can't say that they're terribly helpful for what you're trying to get answered -- but my message to your IT admins would be: version 1.112 would have been released in the Spring of 2014. Given the rate of progress in genomics software, rest assured that over 2 years' worth of changes to Picard is a substantial amount of improvement that deserves upgrading, without a shadow of a doubt. These tools are under very active development and I would recommend upgrading every quarter at least to take advantage of that -- with a clear versioning system to enable users of the system to stick with the same version within a project if that's important to them.

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