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

[MissDona]

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!

[Simon Anders]

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.