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Do we need to implement baseRecalibration before creating Panel of Normal?

sjin_lee09sjin_lee09 SingaporeMember

I am wondering if I need to perform base recalibration on the normal bam files before I proceed with creating the panel of normals, which will then be used for somatic mutation calling with MuTect2.

The tutorial (https://software.broadinstitute.org/gatk/documentation/article?id=11136) and the documentation (https://software.broadinstitute.org/gatk/documentation/article?id=11127) suggest to me that baseRecalibration is not required, but I wanted to confirm before proceeding with the pipeline.

Sangjin Lee



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