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Does BWA expect phred-33 or phred-64 (or something else) type quality scores for input?
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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 -
Hrm, I fail to find the information in the manual. Output is phred-33, but input?Comment
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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).Originally posted by maasha View Post
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Thanks dawe,
I just needed to be sure about the input.Comment
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