The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Depth of coverage in GATK 4
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!