Hello! Now I'm dealing with bulk DNA-seq data.
Firstly, I aligned it to human genome by bwa-mem.
Before MarkDuplicates by picard with only required options(I, O, M), its mean depth of total region is 34.
However, after Markduplicates, its mean depth of total region is only 18! Moreover, after MarkDuplicates, its bam file is only 1G smaller. Why has the depth descreased so much? The depth is calculated by mosdepth (mosdepth -t 4 -n).