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more info on --forceValidOutput in GATK v3.5

timflutretimflutre Montpellier, FranceMember

Hello,
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.

Best,
TF

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