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Check out the documentation at DepthOfCoverage.
@Geraldine_VdAuwera, thank you for your tireless maintenance of the GATK forums and documentation. Could I ask for some clarification on the DepthOfCoverage tool bulletin and its docs?
If I'm not mistaken, this posting was made for the DepthOfCoverage tool/walker? But the URL points to the VariantAnnotator annotation.
Here is the tool documentation link:
Second, in the tool documentation itself: the command line example calls the walker as "-T Coverage" but GATK says no such walker exists. That should be "-T DepthOfCoverage", yes?
Ah, yes, there was a mixup because at the time we had an annotator and the tool itself that had the same name, so the automated system that builds the tech docs got confused. Thanks for pointing this out, I'll correct the link here.
And you are correct that the tool command line example should say -T DepthOfCoverage. That must have been a side-effect of when we renamed the annotator module to just "Coverage" to disambiguate the two. I will correct that as well.
Geraldine Van der Auwera, PhD