Back in the day, I used to have a list of bam files (bam.list), a list of exome targets (targets.bed), a reference (ref.fa) and I could get per-sample coverage depth summary in GATK3:
GenomeAnalysisTK.jar -T DepthOfCoverage -R ref.fa -I bam.list -o samples.depth -L targets.bed --omitDepthOutputAtEachBase --omitIntervalStatistics --omitLocusTable
How do I do this in GATK4?