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  • GATK in Galaxy

    Dear Users,

    I am running GATK (beta ) Unified Genotyper module in galaxy local interface to get the indels and SNP.

    I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i link the reference genome in .loc file (gatk_sorted_picard_index.loc). I could see the Name i mentioned in the .loc file is appearing in the galaxy page while choosing the Reference genome.

    Now while running GATK in galaxy , The command runs for a while and gives ERROR as (The fasta file you specified (/tmp/tmp-gatk-Jjg9Mi) does not exist.)

    Could anybody suggest on the same..

    Thanks
    Sridhar

  • #2
    try GATK on it's own.

    Comment


    • #3
      hello Jackie,
      Thanks for the reply.. i could run GATK in commandline, i am getting results in commanline option but my task is to run it on galaxy.. so i am trying on it..

      Could you please suggest on the same..

      Thanks
      Sridhar

      Comment


      • #4
        Sridhar,

        Were you ever able to resolve this problem? I am having the same issue.

        Comment

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