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  • samtools pileup and tview

    Hello all,
    I used samtools pileup command with –c option. Based on the manual the consensus quality, SNP quality and RMS mapping quality of the reads covering the site are added as 3 columns. But I don’t quite understand how these qualities are defined. And what does RMS mapping quality means? I could not find relevant information anywhere.
    Also the manual says that ‘An indel occupies an additional line. Each indel line consists of chromosome name, , the genotype, .., the first alllele, the second allele,..’ The problem is that I frequently see inconsistency between the genotype and the second allele, such as the line 1, 2 and 4 in the following chunk from the pileup file.

    genotype first alllele second allele
    +G/+G +G *
    +G/+G +G *
    */+T * +T
    */+A * +A
    */* * +G

    I would really appreciate any suggestions/comments.

    Moreover, I had some problem with tview. I posted the problem in the sticky SAM thread, and lparsons reported the same problem next, but we got no response so far. Here is my old post again:
    I tried samtools tview to browse the alignment results in bam format. However, several keys do not work, including:
    Arrows Small scroll movement
    J, K Large scroll movement
    backspace Scroll back one screen
    ..
    I haven’t checked other keys. But would like to report what I saw. BTW, is there any other ways besides tview to view the alignment results in sam/bam format? Thanks a lot!

  • #2
    pparg, did you get the answer about the inconsistency between genotype column and the 2nd allele column? I have same question.

    Comment


    • #3
      Unfortunately, I haven’t got the answer so far. You may want to contact the author of samtools. Good luck.

      Comment


      • #4
        Originally posted by pparg View Post
        Hello all,
        I used samtools pileup command with –c option. Based on the manual the consensus quality, SNP quality and RMS mapping quality of the reads covering the site are added as 3 columns. But I don’t quite understand how these qualities are defined. And what does RMS mapping quality means? I could not find relevant information anywhere.
        http://sourceforge.net/apps/mediawik..._pileup_output.

        Also the manual says that ‘An indel occupies an additional line. Each indel line consists of chromosome name, , the genotype, .., the first alllele, the second allele,..’ The problem is that I frequently see inconsistency between the genotype and the second allele, such as the line 1, 2 and 4 in the following chunk from the pileup file.

        genotype first alllele second allele
        +G/+G +G *
        +G/+G +G *
        */+T * +T
        */+A * +A
        */* * +G

        I would really appreciate any suggestions/comments.
        You may understand the "first allele" as the "first candidate allele".

        Moreover, I had some problem with tview. I posted the problem in the sticky SAM thread, and lparsons reported the same problem next, but we got no response so far. Here is my old post again:
        I tried samtools tview to browse the alignment results in bam format. However, several keys do not work, including:
        Arrows Small scroll movement
        J, K Large scroll movement
        backspace Scroll back one screen
        ..
        I haven’t checked other keys. But would like to report what I saw. BTW, is there any other ways besides tview to view the alignment results in sam/bam format? Thanks a lot!
        Capital J,K should always work. I have not seen any exception so far. Arrow and backspace sometimes do not when your terminal is not configured properly. Many viewers are available now for BAM as you can see from this forum.

        Comment


        • #5
          Originally posted by pparg View Post
          Hello all,
          BTW, is there any other ways besides tview to view the alignment results in sam/bam format? Thanks a lot!
          Try igv from broad: http://www.broadinstitute.org/igv/
          -drd

          Comment


          • #6
            Originally posted by lh3 View Post
            Capital J,K should always work. I have not seen any exception so far. Arrow and backspace sometimes do not when your terminal is not configured properly. Many viewers are available now for BAM as you can see from this forum.
            Capital J,K not working here either (samtools-0.1.9)

            Where can I find the keys for tview?
            Homepage: Dan Bolser
            MetaBase the database of biological databases.

            Comment

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