Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

need GenePattern modules for the latest Picard tools

splaisansplaisan Leuven (Belgium)Member ✭✭

(repost of part of a mail to Picard team)

Is there someone out there having new GP modules for as many as possible Picard.jar subcommands (I love them all)

I am preparing a variant training for the fall on our institute in-dev-Genepattern server and would love to teach people use the new Picard as often as possible (and when it opens, will also love to add GATK v4).

The problem for Picard tools is that the java command has changed from a ‘command.jar’ to a ’picard.jar subcommand’ and some arguments may have been added or modified which makes the process of old GP module recycling useless.

The good news is that the new core argument syntax has been made uniform, it may therefore be better to start from scratch and create a generic GP module that fits them (almost) all??

If someone could provide such basic module (or more :-), it would be greatly appreciated.

Best Regards,
Stephane

(VIB: www.vib.be)

Best Answer

  • splaisansplaisan Leuven (Belgium) ✭✭
    Accepted Answer

    This is great news Geraldine, thanks.
    Guy here made already a few wrappers using perl in order to handle exceptions and check inputs before submission. Some limitations in GP input possibilities made this relevant to have an elegant and intelligent interface.
    Thanks for the great tools, I cannot wait to run 4.0 and start to share this with non-academics.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Hi Stephane, when we release GATK4 (beta will be here very soon) the Picard tools will be exposed through the GATK executable, and we'll have JSON descriptor files for each tool (like we already have for GATK3) that can be used to generate wrappers much more easily.
  • splaisansplaisan Leuven (Belgium)Member ✭✭
    Accepted Answer

    This is great news Geraldine, thanks.
    Guy here made already a few wrappers using perl in order to handle exceptions and check inputs before submission. Some limitations in GP input possibilities made this relevant to have an elegant and intelligent interface.
    Thanks for the great tools, I cannot wait to run 4.0 and start to share this with non-academics.

Sign In or Register to comment.