Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

GATK Staff

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.


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