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Depth of coverage in GATK 4

scottfrodscottfrod Salt Lake City, UtahMember


I'm trying to find the depth of coverage for a targeted sequencing project using GATK 4, but I'm confused about which tool I can do this with. I've combed over the list of new tools and have tried the CollectHsMetrics and CollectFragmentCounts tools. Are these the "new" DepthOfCoverage tool of GATK 3.8? What is everyone else using for DepthOfCoverage using GATK 4? Any guidance or tips would be appreciated. Thank you!



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