About base quality recalibration

NanNan Baton RougeMember

I am a newbie for GATK.I do have a question,maybe stupid.But I want an answer.
Why will base quality recalibration come after the indel realignment.It seems that recalibrating the base quality first will be better, because the bam file will be filtered before indel realignment.


Sign In or Register to comment.