I want to run samtools depth with the -a flag to capture positions with 0 coverage.
However due to the circumstances I do not have bam files with the duplicates removed. I realize I can run rmdups but we chose not to due to financial and time constraints (analyzing 1000s of whole genomes on cloud service)
So I would like to ensure I'm not counting duplicate reads with the samtools depth command. Is it possible to use a flag for this?
I would also like to include the -a flag because positions with 0 coverage are informative for my analysis.