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  • Dindel

    hello ,recently,i have used the Dindel 1.01,but in the stage1,the stage1_dindel.variants.txt is empty!!!!
    i don't kown how to solve the problem..bam and bam.bai ;fa and fa.fai are exists!!!
    i haven puzzled for a long time,wish someone can help me !!!!!

  • #2
    What is the exact command that you used, and do you get any error or diagnostic messages? Also what about the libraries.txt file, is it also empty?

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    • #3
      sorry,only the stage1_dindel.variants.txt is empty.
      my command is like this :./dindel-1.01-linux-64bit --analysis getCIGARindels --bamFile ./500.bam --outputFile stage1.Dindel --ref ./fa
      the fa.fai and bam.bai are exists!!
      for no error massege so i don't know what is the matter!!

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      • #4
        try indexing both the reference and bam file with the latest samtools.

        I had the same problem because I generated the index files using some other program and tried running it and I got empty an empty file too.

        But after indexing with samtools it worked.

        hope that helps

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