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  • BWA dbwtsw to Samtools Pileup - what is the score?

    Hi everyone I am using Samtools pileup after doing a bwa-dbwtsw alignment. The output came in this way

    Contig 884 T T 229 0 25 67 ....,,,,.,.,,.,,,.,,,,.,,....,,,.,..,.,,.
    ,.,..,....,,,..,,,,,,,..., =@@<EI???DE??F?=DA?FFFDDFDD?D?EEAF?@?D?F7??EFICIIEI@A@>DA@@@@@CF>;?

    Correct me if i am mistaken, I guess 229 should be the score? What is the scoring system? How should I interpret this score?

    thanks!

  • #2
    Hello,
    I believe this link would be helpful to you.

    http://sourceforge.net/apps/mediawik..._pileup_output.

    Comment


    • #3
      Thanks for the website but what actually is a "Phred-scaled likelihood"?
      Moreover, if the data are generated by solexa, the "Phred-scaled likelihood" would not jump up to 200 something, so that's why I am kind of curious with this.

      So I suppose the higher the score, the better the basepair quality?

      Comment

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