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!
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!
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