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  • bam2pindel Error

    Hi,

    I am trying to use bam2pindel using this command:
    perl bam2pindel.pl -i ./sorted_ByName.bam -o ./pindel -s s79757 -pi 400

    It gives me this error:

    Code:
    Forked pipe to run: /home/medhat/bin/samtools view sorted_ByName.bam
    Error while processing: /home/medhat/bin/samtools view sorted_ByName.bam
    EVAL ERROR: Use of uninitialized value in array element at /home/medhat/source/pindel/pindel/Adaptor.pm line 92, <$PROC> line 1.
    
    CHILD ERROR: 0
    
    Reads in buffer:
    $VAR1 = [];
    
    Broke at record 1
     at bam2pindel.pl line 341
    	main::run_parser('HASH(0x18ac4e0)') called at bam2pindel.pl line 83
    any idea?
    Thanks in advance
    Last edited by Medhat; 02-11-2015, 01:18 AM.

  • #2
    Hi,

    I have exactly the same problem. Did you manage to fix it ? If yes, how ?
    If other people have an idea on what can explain it, their help is welcomed

    Thanks to all

    Comment


    • #3
      Bumping this, as I am getting the exact same message and I haven't been able to find any mention of this error elsewhere on the internet.

      My data is aligned using BWA, converted to a BAM file using samtools normally, and sorted the way the program suggests.

      Any help would be welcomed.

      Comment


      • #4
        Hi all,

        Very late to the party. I've been getting the same error message when trying to run bam2pindel. Has anyone managed to solve it? I emailed Kai Ye but he has yet to reply.

        Comment

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