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  • lukas1848
    Member
    • Jun 2011
    • 54
    #1

    samtools rmdup error

    Hi,

    I am trying to run samtools rmdup on a bam file and I get the following error messages.

    [bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2107:2691:8134'. Continue anyway.
    [bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2208:17576:79909'. Continue anyway.
    [bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2301:18313:189015'. Continue anyway.
    [bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2307:15133:98183'. Continue anyway.
    [bam_rmdup_core] inconsistent BAM file for pair 'HWI-ST1027:65: D03FGACXX:4:2301:4254:2861'. Continue anyway.
    I googled and didn't find anything on that, so I hope that someone here might be able to help me.


    edit: just some additional info. I mapped 100 bp PE Illumina reads with stampy&bwa.
    Last edited by lukas1848; 05-08-2012, 03:08 AM.
    Tags: None
  • airtime
    Member
    • Jan 2011
    • 14
    #2
    Hi,

    did you sort your bam file before?
    Some further proceeding steps would be helpful (like full command execution).

    Comment

    • lukas1848
      Member
      • Jun 2011
      • 54
      #3
      I sorted my bam files
      samtools view -uS ACAGTG_001.sam | samtools sort - ACAGTG
      and removed the pcr dups like this

      samtools rmdup ACAGTG_001.bam ACAGTG_001_rmdup.bam
      If I use the -S option in rmdup to force treating PE reads as SE reads, the error does not occur (which seems not really surprising, though)

      Comment

      • airtime
        Member
        • Jan 2011
        • 14
        #4
        Hi,

        ok. How big are your files and your RAM? If you convert sam to uncompressed bam is their size similar?

        regards Air

        Comment

        • lukas1848
          Member
          • Jun 2011
          • 54
          #5
          I used a m1.large EC2 instance, so I had 7.5 gb ram. The sam files are ~2.2 gb each. The uncompressed bams are 1/4th of the sam files' size.
          Is this somehow suspicious? I mean, should uncompressed bams be of roughly the same size as the sam template?

          I am thinking about trying out Picard's duplicate removal, but I want to make sure first that my bam files are correct.

          Comment

          • lukas1848
            Member
            • Jun 2011
            • 54
            #6
            I contacted the authors of stampy and they said that they occasionally record errors of that kind but that it does not show any ill effects. According to them, samtools is complaining without good reason.

            I think I'll just go with that, even if it still is odd though.
            Last edited by lukas1848; 05-09-2012, 06:38 AM.

            Comment

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