How to calculate depth of coverage and applying read depth filter

Question

[Sd]

I want to calculate coverage for a CRAM file. I want to see how the coverage varies by chromosome in different genomic regions and apply filters for 1X, 10X, 20X, and 30X to compare the results. For example, applying a 10X filter means calculating and providing genomic regions with at least 20 read depth, excluding regions with below 20 read depth, and then providing coverage results. Is there a way to do this using samtools depth, samtools coverage, or any other tools?

Answer 1

[ATpoint]

You can do that with https://github.com/brentp/mosdepth as a starting point and then postprocess the output.