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  • Picard tools - CreateSequenceDictionary

    Hi there,

    My goal is to use picard tools to estimate % on target rates for a recent target enrichment experiment we performed. Collecthsmetrics seems like a good tool for the job, and so I installed picard to use at the command line. That tool requires that I use the BedtoInterval command, which needs a .dict file from CreateSequenceDictionary. I downloaded my reference fasta file, but am struggling to get CreateSequenceDictionary to run.

    Usage example:

    java -jar picard.jar CreateSequenceDictionary \
    R=reference.fasta \
    O=reference.dict

    My attempt:
    '''gacarson$ java -jar picard.jar CreateSequenceDictionary \ reference.fasta'''
    ERROR: Invalid argument ' reference.fasta'.

    I've also tried putting 'R=' in front of my file name with no luck.

    Any suggestions on how to get this working?

    Thanks for the help.

    Cheers,

    -Glenn

  • #2
    solved! It was that \ that was killing it. I thought that \ was needed in the code.

    '''java -jar picard.jar CreateSequenceDictionary R=reference.fasta''' worked!

    feel free to delete the thread, or leave it so it's searchable

    Comment


    • #3
      Thanks for posting the solution.

      Comment

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