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  • peshon
    Junior Member
    • Jul 2011
    • 3
    #1

    Pindel0.2.4 -c ALL

    I'm having problem running Pindel0.2.4 to call variants in the exome data.

    1) I prepare the configuration txt file.
    /path to/sample_sorted_rmpcrdup.bam 300 sample_name

    2) I tried running pindel.
    "pindel -f ref.fasta -i conf.txt -c ALL -o prefix"

    3) i always get the results for only chr1, for chr2 (and after (chr2,3,4,....)) was no result.
    No currentState.Reads for chr2 found in /path to/sample_sorted_rmpcrdup.bam
    BAM file index 0 0
    There are no reads for this bin.

    4) Then, I tried running pindel only chr2.
    "pindel -f ref.fasta -i conf.txt -c chr2 -o prefix"

    5) I get the results for chr2 as well as chr1 at -c ALL.

    What have i done wrong?
    How can i get all chromosome data?
    Thanks
    Tags: None
  • KaiYe
    Senior Member
    • Jun 2009
    • 133
    #2
    hi

    We noticed the same problem on some BAM files, not on others. We are not sure about the cause but we are working on the solution.

    We will keep you posted, before this weekend.

    Kai

    Comment

    • KaiYe
      Senior Member
      • Jun 2009
      • 133
      #3
      Originally posted by peshon View Post
      I'm having problem running Pindel0.2.4 to call variants in the exome data.

      1) I prepare the configuration txt file.
      /path to/sample_sorted_rmpcrdup.bam 300 sample_name

      2) I tried running pindel.
      "pindel -f ref.fasta -i conf.txt -c ALL -o prefix"

      3) i always get the results for only chr1, for chr2 (and after (chr2,3,4,....)) was no result.
      No currentState.Reads for chr2 found in /path to/sample_sorted_rmpcrdup.bam
      BAM file index 0 0
      There are no reads for this bin.

      4) Then, I tried running pindel only chr2.
      "pindel -f ref.fasta -i conf.txt -c chr2 -o prefix"

      5) I get the results for chr2 as well as chr1 at -c ALL.

      What have i done wrong?
      How can i get all chromosome data?
      Thanks
      Please check out the new version. It is fixed.
      svn checkout https://trac.nbic.nl/svn/pindel pindel

      Kai

      Comment

      • peshon
        Junior Member
        • Jul 2011
        • 3
        #4
        Thank you very much for your quick response!

        Comment

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