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I would be happy to patch it, except that I can't patch it in GATK 4 until CombineVariants is actually added, and if I patch it in GATK 3 then it won't ever be published. Is that not the case?
I've verified that this is broken in GATK 3.6 and 3.8, and CombineVariants is not implemented in GATK 4 so I suppose I'll have to implement this myself
Looking around, this seems to be the same issue as https://gatkforums.broadinstitute.org/gatk/discussion/2165/combinevariants-filteredinall
That thread seems to recommend adding the key to the header, but in this case the key shouldn't need to be there since it's part of the VCF spec. I can look into GATK4 but it's very difficult for us to upgrade versions at the moment.
I'm glad there's a workaround for this. However, is it true that this only works if the File is declared by itself, and not as part of a compound object? Because I've been trying to pass around BAMs and their indices as a Pair (e.g. Pair[File, File]…
Thanks for pointing out the metadata endpoint, that answers my question. Although /metadata doesn't seem to list the actual commands that are being run, which might also be helpful. Is this stored anywhere?