Dear GATK team.
I conducted GATK pre-processing using GATK 4.0.2.
I have some questions.
I used wxs ngs data for mutation calling.
Do you recommend I use exome interval bed when I use Recalibration (BaseRecalibrator)?
Yes, the doc from GATK3 still applies in GATK4.
In shelia's doc,
Is this comment valid in gatk4 pre-processing?
I'm so sorry for delay.
Thanks so much for letting me know!