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How to get the min, max and average coverage for whole intervals (pre-defined in a bed file)?
I am working with DNA sequencing data (illumina). We use targeted sequencing mostly. I analysed the data following your best practice using GATK 126.96.36.199.
My question is: How can I simply generate a report where I can see, for each selected interval in a bed file, the minimum, maximum and average coverage. The available tools under "Coverage Analysis" and "Diagnostics and Quality Control" don't seem to provide such information. I think those tools were available under GATK3.8 but I can't see which ones in GATK4 are replacing them.
Thanks in advance