Malformed VCFs don't generate an error message.

[alanhoyle]

We have some VCF-like files which had some INFO and FORMAT headers omitted. When Oncotator runs on these, it drops any of the data associated with those missing headers, but, as near as I can tell, does this silently. It's not until after the oncotator has finished and we try to look into the VCFs that we notice that it's missing the information we're looking for.

[alanhoyle]

Other than fixing the headers in VCF, is there any way to just tell oncotator to just let the data pass through into the output?

[LeeTL1220]

Not easily, we did make a design decision that Oncotator did not have to honor fields that were not in the VCF header. Under the hood, handling arbitrary fields was surprisingly difficult for internal consistency -- especially for those using Oncotator to convert between VCF and MAF.

…

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