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  • doc.ramses
    Member
    • Jan 2011
    • 26
    #1

    using snappy java in picard tools

    Hey,

    I have a problem using picard-tools on large files. It tells me that I don't have snappyjava in java.library.
    I'm not so familiar with java. Can anyone please point me on how to fix this.
    I've already come across this:

    picard
    http://sourceforge.net/apps/mediawiki/picard/index.php?title=Using_Snappy_in_Picard
    Download picard for free. A set of tools for working with high-throughput sequencing data. A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team


    documentation, but don't really get.
    I'm on a mac os x 10.6.8

    Thank you for your help!
    Tags: None
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283
    #2
    A quick fix is to run "java -Dsnappy.disable=true -jar ...", which will disable snappy, making Picard slower. But at least you don't have to run around trying to get snappy installed correctly!

    Comment

    • doc.ramses
      Member
      • Jan 2011
      • 26
      #3
      Thanks for the quick fix, that works for me. Although really slow

      Comment

      • Graham Etherington
        Member
        • Apr 2010
        • 22
        #4
        Snappy comes distributed with the most recent versions of picard-tools (v1.53 - http://sourceforge.net/projects/picard/files/)
        It's in the top-level directory by itself. The remaining picard jar files are in a sub-directory.

        Comment

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