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  • question about samtools mpileup -6

    Hi,

    Can anyone please tell me when to use this option? I am a bit confused about this. I have sequence data with Illumina 1.8 encoding and have aligned them to generate bam files. In the documentation of mpileup, it says

    -6 Assume the quality is in the Illumina 1.3+ encoding.

    But I don't know if bam files have such encoding issues..

    Thanks!!!

  • #2
    I think it means if you have the qscores in the former illumina format then use this option. Since your data is based on Illumina 1.8+ which i believe is in the Sanger qscore format already, then you don't need to use it.
    Here is a reference explaining qscore differences:

    Comment


    • #3
      That's what I guessed, although still got confused by the "+" in the "1.3+"...
      Thanks!

      Comment

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