Picard or GATK tools

Hi,

some picard tools like MergeSamFiles were ported to GATK 4 beta. Now in the release version they are described as picard tools again. Even though they are part of the GATK and can be used as such.

see here:
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_sam_MergeSamFiles.php
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.5/org_broadinstitute_hellbender_tools_picard_sam_MergeSamFiles.php

Which one should I use? Will there be documentation for the GATK versions?

Thanks and best regards,
Daniel

Best Answers

  • SkyWarriorSkyWarrior TurkeyMember
    edited January 24 Accepted Answer

    Just use plain Picard for now. There seems to be a bug in Picard infused in GATK4.0 and fails at certain operations. A bug fix version may show up sometime.

    https://github.com/broadinstitute/gatk/issues/4135

Answers

  • SkyWarriorSkyWarrior TurkeyMember
    edited January 24 Accepted Answer

    Just use plain Picard for now. There seems to be a bug in Picard infused in GATK4.0 and fails at certain operations. A bug fix version may show up sometime.

    https://github.com/broadinstitute/gatk/issues/4135

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @dbecker
    Hi Daniel,

    The Picard tools that are integrated in GATK4 do have documentation. You can find them in the tool docs.

    -Sheila

  • dbeckerdbecker MunichMember

    Hi,

    Thanks for the information!

    Since the documentation isn't completely perfect yet and still worked on
    (VariantFiltration: --filterExpression in Useage example vs --filter-expression in arguments list),
    I thought it might be something that will appear in time.
    Are those that were part of 4b5 going to be part of GATK4.X.X.X at any point?

    Best,
    Daniel

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @dbecker
    Hi Daniel,

    Thanks for pointing out the VariantFiltration doc error. I will fix it soon.

    I think any tools that were part of GATK4 beta that are not in GATK 4.0.0.0 are deprecated. Are there any specific tools you are interested in?

    -Sheila

    Issue · Github
    by Sheila

    Issue Number
    2902
    State
    open
    Last Updated
    Assignee
    Array
  • dbeckerdbecker MunichMember

    Hi,

    The only tool I use is MergeSamFiles. It's no big problem to work with picard, but it's another tool we have to keep up to date. Since we are working in diagnostics, we also have to keep every version available so we can reproduce our results at any given time with an old pipeline. So it would be nice to only use one toolkit.

    Best,
    Daniel

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
  • dbeckerdbecker MunichMember

    Hi,

    the Usage example says:

    java -jar picard.jar MergeSamFiles
    

    so it is still a picard tool, isn't it?

    Best,
    Daniel

    Issue · Github
    by Sheila

    Issue Number
    2969
    State
    closed
    Last Updated
    Assignee
    Array
    Closed By
    chandrans
  • dbeckerdbecker MunichMember

    Hi,

    No problem. Thanks for the clarification.

    Best,
    Daniel

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