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  • BWA FASTQ input score type

    Does BWA expect phred-33 or phred-64 (or something else) type quality scores for input?

  • #2
    I'm pretty sure it expects Sanger FASTQ format (PHRED scores encoded with an ASCII offset of 33). This will matter if you output SAM/BAM format.

    See also http://bio-bwa.sourceforge.net/bwa.shtml

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    • #3
      Hrm, I fail to find the information in the manual. Output is phred-33, but input?

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      • #4
        Originally posted by maasha View Post
        Does BWA expect phred-33 or phred-64 (or something else) type quality scores for input?
        bwa does not care about scoring at alignment time. phred scores are used only for trimming and phred-33 is the expected scale. If you have phred-64 scaled data and you don't want to convert them before alignment, you can try to apply this patch I wrote for bwa sources. The patch is not official and not aligned with svn versions of bwa. it adds a flag '-I' to aln predicate, to support phred-64 in input (and write phred-33 in output).
        d

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        • #5
          Thanks dawe,

          I just needed to be sure about the input.

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