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Picard tools understand CRAM format natively so you can simply use
CollectWGSMetrics. If not CRAM can be converted to BAM on fly and then fed into Picard.Thanks.. is there any explanation on how Picard calculates the metrics - does it include/exlude dups, soft clipped reads, etc ?
Do you mean the total number of aligned reads in the file or the total number of overlapping bases across an interval? Have you looked at mosdepth?
I meant total number of overlapping bases across the whole (human) genome.. does mosdepth output the overlapping bases ? I did not see that output/option on its git repo