The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
About base quality recalibration
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.