Overlapping bases count in WGS

Question

[NB]

Hi, Is there a way to extract or calculate the total number of overlapping bases from a CRAM file for paired-end WGS ?

If I get the concept right, it can also be calculated by creating a fragment length count file and read length ?

Thank you

[GenoMax]

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.

[NB]

Thanks.. is there any explanation on how Picard calculates the metrics - does it include/exlude dups, soft clipped reads, etc ?

[WouterDeCoster]

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?

[NB]

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