more info on --forceValidOutput in GATK v3.5
according to the release notes, GATK v3.5 has a new engine-level option "--forceValidOutput" to enforce v4.2 of the VCF specifications.
How does this option work? For instance, does it replace missing genotypes in the GT field from "." to "./."? (This is required by Beagle v >= 4.0.)
I don't see information about this option on the "CommandLineGATK" page.