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  • Forget to add "-I" option while run bwa aln

    Hi all!
    As mentioned in the title, I forget to add option "-I" while running bwa aln(my data type: illumina whole exome sequencing data, Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at ASCII 64 ).
    Will it have other major repercussions in addition to the incorrect estimation of quality scores? I plan to use GATK PrintReads (with the -fixMisencodedQuals tag) to fix it, don't know if that's enough.
    Thanks a lot!

  • #2
    1. Double-check that you really would have needed the '-I' option. Illumina data from pipeline versions prior to version 1.8 have the 64-based encoding, since a while, they use 33-based encoding.

    2. The main effect will be that bwa will assume that your reads are much higher quality than they are. Hence, for example, if we end of a read is low quality, it might fail to try to trim (soft-clip) the end to find a match.

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