I am updating our workflow from GATK3.x to GATK4.x. The current protocol depends on the refined bam files generated ("This app outputs the refined (deduplicated, realigned, and recalibrated) mappings in BAM format (*.bam), as well as the associated BAM index (*.bai).") to obtain pileup files for coverage analysis. Therefore I am wondering, if I use the setting below will GATK4 refine the input bam file and use it to generate the pileup file. Do GATK4 vs. GATK3 have similar performance in this case? Thanks.
gatk Pileup \ -R reference.fasta \ -I input.bam \ -O output.txt
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