I have a BAM file, I'm looking to compute the coverage for each contig and a general coverage (so I'm looking for a number like 50X).
What is the best method ?
Please don't post the same question multiple times: What is the best way to compute scaffold coverage ?
There are a bunch of options in this thread: Tools To Calculate Average Coverage For A Bam File?
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.