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depth of coverage from gVCF files
I have a large number of gVCF files, either single samples or combined in approximately 100 samples per combined gVCF file.
I would like to compute something like the average depth for a set of regions of interest from the combined or single gVCF files.
I can see that I could try to get a VCF output at every position, and use that to infer the percentage with a given read depth, but that seems mightily cumbersome.
So my question: is there an equivalent to the DepthOfCoverage GATK module that takes as input gVCF files? ideally combined gVCF and extract per sample average/median/minimum depth but otherwise I can work with single sample gVCF data.
Thank you in advance