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I am confused about the Command-line Argument, --downsample_to_coverage.
How do I know if the walker is "locus-based" or "non-locus-based"? Your on-line guide page gives an example of each but not how to identify one type of walker from another.
This is specified in the technical doc page for each tool; for example on the tech doc for BaseRecalibrator you see Traversal ReadWalker.
Geraldine Van der Auwera, PhD