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  • mboursnell
    Member
    • Jul 2012
    • 17
    #1

    IndelRealigner ERROR

    Whe I run IndelRealigner I get an ERROR like this. It is a whole screen of chrUn something, ending like this:

    chrUn_AAEX03026059, chrUn_AAEX03026060, chrUn_AAEX03026061, chrUn_AAEX03026062, chrUn_AAEX03026063, chrUn_AAEX03026064, chrUn_AAEX03026065, chrUn_AAEX03026066, chrUn_AAEX03026067, chrUn_AAEX03026068, chrUn_AAEX03026069, chrUn_AAEX03026070, chrUn_AAEX03026071, chrUn_AAEX03026072, chrM]
    ##### ERROR ------------------------------------------------------------------------------------------

    The command is this:

    java -Xmx8g -Djava.io.tmpdir=javatempdir -jar GenomeAnalysisTK.jar -T IndelRealigner -R canfam3.fasta -I ABC.realigned.rg.bam -targetIntervals ABC.bam.intervals -o ABC.clean.bam -known dummy_DBSNP.vcf -compress 0 -model USE_READS


    Any ideas? It all works OK with canfam2 so it seems to be something to do with the canfam3 REF sequence.
    Tags: canfam3, gatk, indelrealigner
  • DZhang
    Senior Member
    • Jun 2010
    • 177
    #2
    Hi mboursnell,

    Please check if "chrUN..." and "chrM" are in your reference sequence used in mapping.

    Best regards,
    Douglas
    https://www.contigexpress.com

    Comment

    • mboursnell
      Member
      • Jul 2012
      • 17
      #3
      Yes they both are. chrM only once.

      I think now it's down to the the dummy DBSNP file; I don't what to filter any SNPs but it needs file so I have to make a dummy one. Not sure how to make one that is innocuous...

      Comment

      • DZhang
        Senior Member
        • Jun 2010
        • 177
        #4
        In that case, you do not have to supply -known as it is optional.

        Best regards,
        Douglas
        https://www.contigexpress.com

        Comment

        • mboursnell
          Member
          • Jul 2012
          • 17
          #5
          You're right! I'm sure it used to be required. Maybe that was with UnifiedGenotyper.

          Comment

          • DZhang
            Senior Member
            • Jun 2010
            • 177
            #6
            I believe it helps improve the results if you have a list of known indels.

            Best regards,
            Douglas
            https://www.contigexpress.com

            Comment

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