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  • Column order in samfiles in consensus calling

    the documentation in
    http://samtools.sourceforge.net/cns0.shtml
    is slightly confusing at this portion

    When consensus calling is switched on, pileup command will insert the consensus base, consensus quality, SNP quality and maximum mapping quality of the reads covering the sites between the `reference base' and the `read bases' columns.

    as 'the number of reads covering the site' is actually between the `reference base' and the `read bases' columns. (see http://samtools.sourceforge.net/pileup.shtml )

    I believe the order of the columns should be as per this csv line?

    "chromosome"," 1-based coordinate"," reference base","consensus base"," consensus quality"," SNP quality ","maximum mapping quality "," the number of reads covering the site"," read bases"," base qualities"
    Last edited by KevinLam; 07-20-2010, 02:50 AM.
    http://kevin-gattaca.blogspot.com/

  • #2
    You're right. It seems that the docu is outdated. Several people have also noted the presence of two additional columns for indel lines in pileup that are not explained in the manual or FAQs.

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